(written from a Production point of view)
The following are Star Trek parodies and references in pictorial literature.
After Eden Edit
A creationist comic by Dan Lietha.
In one cartoon, a kid asks a creationist whether he likes Kirk or Picard.
A comic featuring the McPherson family.
After Hammie (around 7 or 8 years old) tries to sign up for a dating service online, his father, Daryl, says he's changing the computer's parental controls from "stun" to "vaporize".
January 15 2018: Wanda describes Zoe and Hammie as having been "going at warp speed all day" (running around really fast)
Calvin and Hobbes Edit
January 25, 1987: After losing to Hobbes in a game of checkers, Calvin accuses the tiger by saying, "You must have used some sneaky, underhanded mind-meld to make me lose!"
June 15, 1987: While imagining having found a magic carpet, Calvin says, "Ok, rug, warp factor five!"
Chief O'Brien at Work Edit
Centaurus is a French language series about a generation ship reaching its destination. It is a collaboration between several high profile sci-fi BD creators, Leo, Rodolphe, and Janjetov. At the climax of the third album of the French language series, "Terre de folie", a control center is with many screens depicting star charts. Among them is The Explored Galaxy. Artist Zoran Janjetov has previously incorporated elements from Star Trek as interfaces in a similar manner in a previous series, The Technopriests.
Coffee With Jesus Edit
In the January 4th, 2017 comic, Jesus encourages man to explore the heavens by saying "Boldly go.".
DC Comics Edit
Over the years, DC comics artist have included multiple visual homages to Star Trek in their art. In the 1970s, one member of the Green Lantern Corps was recognizable as being a Vulcan.  In the 1990s, backgrounds in both "Legion of Super Heroes" and "Legionnaires" included recognizably Star Trek-inspired ships.
Dilbert is a popular newspaper comic featuring an engineer called Dilbert and satirizing corporate and office culture. There is also an animated series, which also features a number of Star Trek references. (documented here)
The comic for August 19, 1993 has a mind-reading Dogbert discovering that all the company employees care for are romance, ski trips and Star Trek. 
The comic for December 13, 1993 has a customer asking if a product will be capable of detecting tachyon field emissions. Dilbert notes that he's confusing the company with Star Trek again, but when a salesperson promises to include it in the next update, Dilbert thinks "Beam me up, Spock, there's no life on this planet". 
The comic for July 25, 1994 has Dilbert remarking that it seems unnatural for him to have an actual girlfriend, because when the captain on Star Trek falls in love, the women always dies in an unlikely accident. 
The comic for March 3, 1996 has Dilbert interviewing a potential new employee. When she looks right through his attempt to portray company culture in a positive light, he panics, his inner thoughts being "My shields are down... a hull breach is imminent". Later Wally also independently identifies Dilbert's state as a hull breach. 
The comic for October 9, 1996 has Dilbert saying "Resistance if futile. You will be assimilated." 
The comic for January 15, 1997 sees Bill Gates' house coming to Dilbert's house yelling "prepare for assimilation" after he accidentally agrees to be Bill Gates' towel boy by not reading a software license. 
The comic for November 15, 1997 has Dogbert recalling a story in which Dilbert yelled "I'm an engineer, not a diamond cutter, dang it!". 
The comic for July 7, 2003 has Carol sarcastically responding to the request that she print out the company website and put it into a binder for easy reference that she will also translate it in Klingon to make it even easier. 
The comic for May 3, 2005 has a character asking Dilbert which of the Star Trek seasons he liked best. 
The comic for November 19, 2009 has Dilbert describing a consultant with pointed ears as a "Spock-eared sociopath". 
The comic for January 13, 2011 again mentions Dilbert and his college Alice being on the same pon farr cycle. 
Dirkjan is a popular Dutch short gag series. The eight album, simply called "DirkJan 8", contains a sizable selection of science fiction themed gags, the majority referencing the original Star Trek. Several characters are translated into original series crewmembers, and gags include feature Klingons, cloaking devices (in the form of hiding your ship behind bushes), Borg (who have developed peculiar speech patterns after assimilating a smurf) transporter accidents, the series writer appearing as a Q like entity, and more.
Donald Duck Edit
The Donald Duck story "Beam Me Up, Mr. Fargone", (D 97619) written by Kari Korhonen and drawn by Vicar, is a spoof of Star Trek, particularly the fandom, conventions and merchandise. The story is set in a science fiction convention. Some of the items sold at the convention include a wooden log labeled "Captain's Log" and a Vulcan ear labeled "Final Front Ear". The creator of the series lives in seclusion, and in a video shown in the convention, tells the interviewers to get a life.
Ensign Sue Must Die! Edit
A Star Trek inspired web comic that draws primarily from the events of the alternate reality movies. Basic premise is that a Mary Sue character who has newly transferred causes mayhem for the crew of the Enterprise. This cartoon has several crossovers with characters from various other films, shows (including The Next Generation), and books, including those portrayed by Star Trek actors. 
The comic Foxtrot has made fun of Star Trek numerous times and the youngest member of the family, Jason, is an avid Trek fan.
In one comic, Jason makes Christmas cookie red shirts. In another, one of his product suggestions for beef jerky is "beef Kirky", jerky in the shape of Kirk's Enterprise. 
Jason had sung Aktuh and Maylota in the shower at least once, making his parents think he was dying.
Geeks & Greeks Edit
General Protection Fault (GPF) Edit
A web comic that pocks fun at the comic industry, Gutters has made a joke or two based on the Star Trek line of comics:
The Hitchhiker's Guide to Star Trek, the Next Generation Edit
The Hitchhiker's Guide to Star Trek, the Next Generation is an Internet cross of Star Trek and The Hitchhiker's Guide to the Galaxy. It was written by David T. Lu and Mickey McCarter. An HTML version of it was made available in 2011.
Jump Leads Edit
The webcomic Jump Leads has referenced Star Trek several times, from mention of a hypothetical "goatee-toutin' doppelgänger" in the first issue, "Training Day", to characters and locations named after actors involved with the production of the various shows, right up to the tenth issue, entitled "The Voyage Home", which features cover art that pays homage to the poster for the movie.
The Book of Bunny SuicidesEdit
This book is a collection of cartoons about suicidal rabbits, includes one cartoon in which a bunny places itself on a transporter next to what appears to be Kirk and Spock, but positions itself half inside and half outside the beam so that when the transporter energizes, only half of it is transported.
De Kiekeboes is a popular Dutch language Belgian comic book series, which despite having a mostly realistic modern day setting has on occasion flirted with science fiction inspired plot elements.
One such elements is the appearance of a holodeck in the album "De truken van Defhoor". The holodeck functions much like the ones in Star Trek, and visually looks like the ones aboard the Enterprise-D.
The now-defunct Hungarian version of Mad Magazine featured a three-issue parody of Star Trek: The Next Generation, entitled Star Tok, in 1999. 
Les Naufragés d'Ythaq Edit
In the twelfth album of this French science fiction comic, "Les Clefs du Néant", a spaceship is commanded by a captain that looks like a slightly gritty version of Spock.
Least I Could Do Edit
The web comic Least I Could Do makes various references to Star Trek, and all other manner of science fiction, throughout the series. These can be seen at their website or in the book collections.
- Make It Not
- Make It So
- Friendly Angel, Come to Me
- He's So... Human
- Gorn Injuries
- Picard Manouever
- Are Tribbles the same as Furries?
- Fruits or Vegetables
- Tears of a Rayne
- Make it so!
- Man the catapults!
- Imzadi Night Stand
- Make it so!!!
- This means something. This is important.
- Beeee goooood
- Give me tactical!
- I though we were sparring
Mad Magazine Edit
Mad Magazine (#115, December 1967) had a parody of Star Trek called "Star Blecch!".  The title alteration followed two parodies of the films and spin-off series.  The October 1976 issue (#186) featured a musical parody called "Keep On Trekkin'", with Kirk, Spock and Alfred E. Neuman dancing on the cover ; thirty-five years later, in June 2011 (#509), that image would appear at the end of Dancing With The Star Wars (a Dancing with the Stars satire using Star Wars characters) advertising a similar Trek treatment the next week - but Kirk and Spock now have the faces of Chris Pine and Zachary Quinto, to which a senile-looking William Shatner, sitting in a motorized scooter onstage, takes great offense. Kirk appeared again, "green woman" in tow, in the very next issue (#510), one of many well-known "captains" (including Morgan, Sparrow, Kangaroo, Sullenberger and Ahab) to whom upcoming film subject Captain America is compared unfavorably; the character's likeness is once again that of TOS-era Shatner. The magazine will frequently insert Trek references into stories with Trek actors: for example, the beginning of the Samantha Who? parody in the May 2008 issue showed Tim Russ's character with Vulcan ears and a Starfleet combadge on his jacket (a later scene showed two Trekkies ogling the main character, played by Christina Applegate), while in a June 2003 parody of the X-Men film X2, Professor X (Patrick Stewart), asked how he could stand to be around so many "mutants", replies that, after enough Star Trek conventions, it was easy - or other science-fiction franchises: Worf, Quark, Odo and Morn could be seen in the background in various parts of a May 1995 X-Files parody, while the beginning of an April 1998 spoof of Alien Resurrection showed a group of famous sci-fi aliens concealed in pods behind the main characters: one of them is Spock, clearly looking in the direction of his mother. Mad has recognized Trek's contributions - on the cover of the November 2002 issue, celebrating the magazine's 50th Anniversary, the fifty different images used to create "5" and "0" include Alfred E. Neuman as a Vulcan (from the "Keep On Trekkin'" cover) and a Ferengi.
Marvel Comics Edit
In the late 1970s and early 1980s, Marvel included Star Trek-inspired characters and artwork depicting members of the Shi Ar Empire, most notably "Captain K'rrk", commander of a multi-species crewed Shi'ar vessel. Their uniforms were depicted in the Trek service division (Command, Science, Operations) colors, using the original lime/olive green for Command. K'rrk, like his Trek inspiration, was promoted to admiral later in his career.
In the late '90s-early 2000s, another Shi'ar captain was introduced as Captain P'crrd. In keeping with his namesake, he was bald.
After their introduction to the Shi Ar, the X-Men incorporated "hard light" technology into their Danger Room training environment, rendering it functionally equivalent to a holodeck.
In one issue of Excalibur, the character Peter Wisdom makes fun of Professor Xavier by being pushed around in a wheelchair and wearing a bald cap, spouting out various Xavier-originated phrases before saying "Make it so!", one of Picard's catchphrases. Ironically, this issue came out long before Patrick Stewart was cast as Xavier.
The Megatokyo comic 1337 has a reference to redshirts.
Mother Goose and GrimmEdit
This comic has several references to Star Trek, including Spock summoning McCoy to the bridge because Kirk had knocked himself silly after setting the laser printer on stun.
My Little Pony: Friendship is Magic (IDW Comics) Edit
In Issue #2, Pinkie Pie finds a pony skull in the Appleloosan Mountains and it names it "Mr. Bones", due to the skull having Leonard McCoy's hair style.
In Issue #9, Princess Luna's shapeshifting t-shirt gains an Starfleet emblem during the race event with Big Macintosh.
In Issue #10, there are some ponies that resemble James T. Kirk and Spock, a gray pony that resembles Bilar tells them, "Joy to you friends! Come for the festival are ya?"; this is a reference to the episode "The Return of the Archons".
In Issue #11, in the basement were Shining Armor plays a game similar to Dungeons & Dragons with his friends, there is a poster that has a Constitution-class refit, possible the USS Enterprise, and the title is "Star Trot II", an obviously reference to Star Trek II: The Wrath of Khan.
In Issue # 16, Rainbow Dash's imagination drops them straight onto the pony version of Star Trek: The Original Series. Naturally, she's Kirk, Twilight Sparkle is Spock, and Rarity is Uhura. There's also a pony version of Yeoman Rand in the background of one shot.
In Issue # 25, when Rainbow Dash asks Twilight Sparkle why Spike isn't carrying Rarity's bags, she tells her that he is currently at a Pony Trek convention.
In Issue # 41, "Rainbow Dash and the Very Bad Day", Zecora's cottage is shown to have a book containing Vulcan script, or a script modeled after it.
In Issue # 71, Bon Bon's Nightmare Night costume is a classic Redshirt uniform.
In Issue # 75, Qo'NoS and Praxis as well as Wolf 359 appeared on a list of planets in the "Andalusian" star system.
In the Micro-Series #10, there are several references in the next order: Princess Luna's pet opossum is named Tiberius, a possible reference to James T. Kirk, during the conference, an Earth pony has a cutie mark with the Starfleet emblem, and at the fair page, there is an airship with the number "1701", referencing the registry number of the USS Enterprise.
In Friends Forever Issue #2, among the various scenarios that Discord puts the CMC through includes a full-on take of Star Trek: The Next Generation.
It has the Cutie Mark Crusaders (Scootaloo, Apple Bloom, and Sweetie Belle) dressed up as Riker, La Forge, and Picard, respectively, and were seen on the bridge of the USS Enterprise. Rarity's cat, Opal, is dressed up as a TNG-era Romulan. When she attacks, Scootaloo shouts that they should "Split the ship in half". Discord is seen at the end of that portion, dressed in Q's judge outfit from "Encounter at Farpoint", musing where he had seen this before.
The 1980s UK children's comic Oink! featured a Star Trek parody photostory, "Star Truck", in its issue dated 31 May 1986. The story concerns the crew of the Star Truck Enterpies: Captain Slog, engineer Jock (with kilt and tam o'shanter) and science officer Sock, in pursuit of Jerm, a chicken-headed humanoid with powers of mind control which he intends to use to conquer Earth. The pursuit causes the characters to pop up in several other strips scattered throughout the issue, before Jerm is finally cornered and regressed to an egg by Sock's time warp ray.
The story, translated into German (and also colorized), subsequently appeared in the first issue of the short-lived German licensed version of the comic, Dr Ruebenschwein's Oink!.
A second adventure, "Star Truck II: The Search For Sock", appeared in The Oink! Book 1988.
Pardon My Planet Edit
Yet another redo of Kirk "going where no man has gone before" 
The February 28, 1972 edition of the Peanuts comic strip involves Linus saying Snoopy should think he'd get bored just sitting on top of his doghouse all day, to which Snoopy replied with "On the contrary. Who could get bored flying the starship Enterprise?"
Penny Arcade Edit
The web comic Penny Arcade make various references to Star Trek throughout the series. These can be seen at their website, or in their book collections.
In the second chapter of the manga The Electric Tale of Pikachu, a loose adaptation of the animated series, Ash mentions that his Pikachu's name is "Jean-Luc Pikachu". Pikachu is also seen to be wearing a Starfleet combadge in the panel in question.
Prayer Pups Edit
A Christian comic featuring dogs.
Nim has a Klingon phrase book.
The web comic Player vs. Player make various references to Star Trek, most notably Star Trek: The Original Series, throughout the series. These can be seen at their website, or in their book collections, of which book five is titled "Treks On".
Saturday Morning Breakfast CerealEdit
This popular webcomic has referenced Star Trek several times.
In one 2011 comic,  the bonus joke accessed by the red button has a geek ineptly trying to diffuse an awkward situation arising from having different favorite Star Wars movies by mentioning "because all of Star Trek is great".
In a 2014 comic,  two kids explore the ethical questions arising from using the transporter, based on the assumption that a transported being would be killed and a clone created elsewhere. They ponder a number of scenarios, and then conclude that while they don't have answers now, "this is the kind of stuff you get all figured out by the time you're a grownup".
Sev Trek Edit
Sev Trek by John Cook, is a web comic parody of Star Trek (as well as many other popular sci-fi shows) from The Original Series to Enterprise. It even spawned a computer animated "episode" of Sev Trek: TNG.
The Short-Timers by Gustav HasfordEdit
Snippers (meaning snippets) is a comic that appears daily in the Dutch newspaper Metro. In one comic, included in the fifth collection album, two people find a toy robot dropped in a park and contemplate the child that is crying at this very moment. In the next panel, a huge geek is seen crying in a room filled with various science fiction merchandise, including what appears to be a Star Trek poster.
Sonic the Hedgehog comic book series Edit
In the Knuckles the Echidna and Sonic the Hedgehog comic book series' produced by Archie Comics, the Echidna character Moonwatcher can be seen wearing a uniform that closely resembles the operations division TNG Starfleet uniforms. Furthermore, with the VISOR-like device over his eyes, he is quite similar in appearance to Geordi La Forge. A later issue introduced the "Battle Cruiser", a massive flying ship used by the Echidna group the Dark Legion. Its designs mimic those of the Klingon Bird-of-Prey, D'deridex-class, and Galaxy-class ships.
It should be noted that both instances were created by Ken Penders, who worked on Star Trek comics in the past.
Suske en Wiske Edit
This is a long-running and very popular Belgian comic book series, of which a handful of albums have been translated under various titles in English (though none of the ones mentioned below).
In the album "De Verradelijke Vinson", a dog which has infiltrated the underground base of a mad scientist thinks that it looks like a space base, something he has seen on TV on something called "Stardrek" (which translates to something like star muck.)
The album "De Tikkende Tinkan" shows at one point various spaceships crashing down all over the world. One frame shows a ship very similar to the original Enterprise crashed into the Eiffel Tower.
Also, the album "Het Lederen Monster" features the usage of a holodeck greatly resembling the one aboard Voyager.
The pre-refit USS Enterprise also made a cameo appearance in the Star Wars comic A Death Star is Born. Also, in the comic book adaptation for the Star Wars novel "Dark Force Rising," a boy on the planet Jomark can be seen holding a model of the Enterprise (Kirk, Spock, and McCoy are also in the frame).
Storm is a Dutch-British pulp science fiction comic book most popular in the Netherlands. The album "The Robots of Far Sied" has Storm saying "beam me up Scotty" as he prepares to be digitized.
Tales From Salonbay: Adventures in Xenocosmetology Edit
A Star Trek inspired webcomic. The main character, Moxie Magnus, is a hairstylist and makeup artist on the Enterprise. Most of the comics feature her offering beauty tips to the various aliens the crew encounters or annoying the crewmembers. 
The Technopriests Edit
In the first issue of this comic book, a few visual references to Star Trek are made. A computer displays a LCARS interface, and later the uniforms of the Techo-pre-school have a remarkable resemblence to original series uniforms.
The World God Only Knows Edit
During Chapter 216 of the Manga "The World God Only Knows", Keima wears a uniform resembling one of starfleet when trying to convince Urara he's an alien.
The web comic xkcd is well-known for its references to geek culture, so it should come at no surprise that it has referenced Star Trek on a number of occasions.
"Quantum Teleportation"  has a researcher lamenting that that the press always connects quantum teleportation research to the transporter from Star Trek, and then always write the same disappointed story when they find out it is not the same thing.
"Numbers"  charts the number of Google results for certain phrases with certain numbers inserted (for example; I'm <x> and have never had a boyfriend"). Among the sentences charted is "There are <x> lights", referencing the famous scene from "Chain of Command, Part II".
"Interstellar Memes"  charts how far certain memes would have traveled given "speed-of-light delay". According to the comic, "Live long and prosper" might have made it to HD 211415 by now, while "Resistance is futile" would have reached Vega.
"Data"  has a character proclaim that after Kirk and Picard, the most popular Star Trek character are Data to annoy a grammar pedant.
"Santa"  has a character using the phrase "the needs of the many..."
"Bracket"  mentions Spock (as well as in an unrelated section, Chris Pine).
"Gnome Ann"  shows part of the legend of Gnome Ann involving a ship reminiscent of the original Enterprise, stating "Our mission, to boldly go where Gnome Ann has gone before".
Y The Last Man Edit
In issue #27, Yorick and Agent 355 walk in the street of San Francisco. Yorick comments that the city doesn't completely suck and says that it is no wonder that the Federation of Planets choose it as its HQ location. Agent 355 doesn't understand his comment, and thinks that it is a Star Wars reference.
The September 28, 2011 edition of the Ziggy comic strip involves a transporter mishap, with a request to Scotty for assistance being heard coming from Ziggy's toilet.
Ziggy Cartoon May 10, 2015