(written from a Production point of view)
Even before the members of the series' main cast were selected, Brannon Braga heard many story pitches, shortly after the series began accepting pitches from freelance writers. Of the scores of pitches he heard, several were passed on to the producers only to be rejected. (Cinefantastique, Vol. 27, No. 4/5, p. 70)
Many undeveloped spec scripts written for VOY were read by Mike Sussman, during an intership he went through on the show, and several that he approved were summarized by him to Michael Piller, as Sussman was required to do as a temporary intern. "The problem is they all sucked," he later remarked. 
Other undeveloped story ideas were suggested by Chakotay actor Robert Beltran, while having a meeting with three writing staffers. "There was Ken [Biller], Brannon [Braga] and Joe [Menosky], we were having dinner and they were asking me what I would like to do and with [the] holodeck with Chakotay," Beltran remembered. "And I gave them some ideas and they said, 'Nah, nah, we already did this or that on Next Generation' [....] What I told them at the meeting was when it comes to sci-fi, everything seems possible, so nothing seems that interesting to me. I said, 'If I chose this thing, I miss out on a myriad of other possibilities, so I would rather it come from you guys.' The several episode suggestions I had, and they weren't really heartfelt, they were just things off the top of my head, so I didn't have any strong feelings about a Chakotay episode." 
Midway through season 7, Kenneth Biller teased a few episodes in early development that didn't come to fruition. One, following a few Chakotay and Tuvok moments in "Repression", would have "put them together again, exploring a kind of archaeological puzzle that turns out to be a lot more than either of them thinks it is. It's kind of a game." Biller noted that Tom Paris would have acquired a holoprogram based on an alien mythology with an icon and a maze of tunnels, that would have turned out to be a big logic problem, resulting in "the two of them [working] on the puzzle together, and it turns out [to be] much more than they realized." (Star Trek: The Magazine Volume 1, Issue 20, p. 23)
Biomimetic lifeforms' homecoming
A story that was under consideration by the writing staff of Star Trek: Voyager involved "Silver Blood" duplicates of the USS Voyager's crew, biomimetic lifeforms that would ultimately appear in the episodes "Demon" and "Course: Oblivion". The undeveloped plot would have featured the duplicates being welcomed "back" to the Alpha Quadrant. (Star Trek: Action!, p. 5; Cinefantastique, Vol. 31, No. 11, p. 49) Jeri Taylor explained, "Everybody thinks that Voyager is home and there are celebrations, and they see their loved ones, etcetera, etcetera. And it turns out to be an invasion or a dark plot of some kind." (Star Trek: Action!, p. 5) Joe Menosky elaborated, "Brannon [Braga] had some great images. One was opening with Voyager above Earth, this great homecoming sequence. There are fireworks in the sky, and everybody is going down to their homecomings. Janeway has a wonderful tearful reunion with Mark. She kisses Mark and she then snaps his neck, end of teaser. Then he had this image of like a thousand Voyagers converging on Earth. Somehow, these duplicate Voyagers were being created that didn't even know who they were." (Cinefantastique, Vol. 31, No. 11, p. 49) According to Jeri Taylor, another of the plot ideas was that the duplicates would arrive, amid great fanfare, at Deep Space 9. (Star Trek: Action!, p. 5)
The story was devised at the end of Voyager's third season. "Writing the teleplay, it just didn't seem to work," said Joe Menosky. "We shelved it, and did 'Scorpion' [and 'Scorpion, Part II'] instead." During the fourth season, the shelved plot was repeatedly reconsidered, as a possible two-parter, but was replaced first by "Year of Hell" and "Year of Hell, Part II", and then (months later) by "The Killing Game" and "The Killing Game, Part II". (Cinefantastique, Vol. 31, No. 11, p. 49) It was also considered as a potentially usable but unlikely fourth season finale, towards the end of that season (specifically, shortly before and on 2 February 1998, just prior to the writing of the actual fourth season finale, "Hope and Fear"). (Star Trek: Action!, p. 5) Joe Menosky commented, "The mimetic aliens got to have this really weird reputation as being a negative muse. It was this weird thing that no one wanted in the room." (Cinefantastique, Vol. 31, No. 11, p. 49) At about the end of the fourth season, Jeri Taylor offered, "The more we discussed it, the more we thought that once they go home, even if it isn't really our characters, well, it undercuts whatever will happen when the real crew actually does get home. Which we do intend to have happen." (Star Trek: Action!, p. 6) Regarding the fact that the alien duplicates of the discarded narrative ultimately turned up in "Demon" and "Course: Oblivion", Joe Menosky concluded, "Ironically, the mimetic alien show became a two-parter in a strange way." (Cinefantastique, Vol. 31, No. 11, p. 49)
Marc Guggenheim story
Jamahl Epsicokhan pitches
In 2000, Star Trek: Voyager reviewer Jamahl Epsicokhan was invited to pitch stories for the series. On 10 March, he traveled to Los Angeles and pitched four stories to Bryan Fuller, all of which were rejected. The pitches were titled "Momentum", "Human Option", "The Warning", and "Do Not Harm".
"Momentum" involved a planet travelling at warp, threatening to destroy an alien medical research facility. "Human Option" was about Seven of Nine suffering an accident, which caused her Borg implants to shut down. "The Warning" would have been about a time-traveling alien, who tried to stop the Voyager from causing a subspace disaster. Fuller rejected this pitch, among other reasons, for being too similar to "Future's End". "Do Not Harm" would have seen The Doctor killing somebody on an away mission, causing an ethical conflict for him. Again, this pitch was rejected for being too similar to an existing episode, this time "Latent Image". 
This story would have seen Voyager mediate a dispute between an asteroid base on a critical mission of mining a substance used in battling an epidemic, and a rogue planet steered into the system by its inhabitants to escape a supernova. The insertion of the planet in its new orbit would wipe out the asteroid belt and thus the base. 
"Human Option" was a story focusing on Seven of Nine who, after an accident, lost seventy-five percent of her Borg nanoprobes. This would have left her more Human. For example, she was no longer able to regenerate and thus had to learn to sleep. However, while Janeway welcomed this opportunity, Seven herself set her sight on a medical procedure that would restart nanoprobe production. The story was rejected by Bryan Fuller because it was too similar to a seventh season story (presumably "Imperfection") which had been broken just a week earlier, in which Seven's Borg regulator failed and and one of the Borg children, Icheb, wanted to donate a piece of technology to save her. 
This story would have seen Voyager lending assistance to a planet suffering the ill effects of a recent wormhole-creation experiment gone awry. Voyager's crew also met an alien, which maintained that any help from Voyager would cause more disaster. Ultimately, the alien tried to stop Voyager himself, causing an event that sent him back in time with only the memory that Voyager had to be stopped, a paradox. The story was rejected as too complex, and the alien's motivations similar to Captain Braxton's in "Future's End". 
"Do No Harm"
This story had The Doctor being forced to kill someone to protect another crew member while on a medical mission of mercy on a war-torn planet. This contradiction of his Hippocratic Oath programming left The Doctor disturbed. He worked through his issues by talking about violence with fellow crew members like former Maquis Chakotay and B'Elanna Torres, and by visiting a number of violent holodeck programs. The story was rejected as being too similar to "Latent Image", and because Bryan Fuller was of the opinion that The Doctor would not be so naive concerning death and violence. (citation needed • edit)
Janeway on trial
"When we were talking story before the season began, I thought, 'One of the shows you should do is the trial of Captain Janeway. You should have the crew, one day, put her on trial.' That would be a real major thing in [the] life of the ship, if the crew can do that, if they really have the power to take command away from her at any moment. If they are really willing to put her under that kind of microscope, it calls into question the entire structure of the show, the entire social fabric, the command structure. Why are we behaving in this way? Why do we hew to these rules anymore? Do the rules still apply to us? What do we find within the rules that work? What do we find that doesn't work? What does it say about Janeway? I thought that there is ground to play there." 
Kes returns again
Early in season 7 (after "Fury"), Biller noted that in the writer's room, "it is occasionally discussed; it is possible" that Kes would return again, "but he wouldn't want anyone to hold their breath." (Star Trek: The Magazine Volume 1, Issue 20, p. 24)
"One Little Ship" precursor
René Echevarria offered Star Trek: Voyager a story about a spacecraft being shrunk and the ensuing events. The story had a long developmental history, as Echevarria had written it as a Star Trek: The Next Generation spec script, unsuccessfully submitted it for that series, then recently submitted it to Star Trek: Deep Space Nine without it being bought for that series either. "I went to [Executive Producer] Brannon Braga, and said, 'If you want to do the show on Voyager, feel free. I think there could be a lot of fun here,'" Echevarria recalled. "He said yes, and he went to [Executive Producer] Rick Berman with it, and Rick said, 'I think you've lost your mind.' So Brannon completely forgot about it." Shortly thereafter, the plot ended up being produced as DS9: "One Little Ship". (Cinefantastique, Vol. 30, No. 9/10, p. 39)
Q on a beach
A Q story for Star Trek: Voyager was pitched by Q actor John de Lancie. Supervising Producer Joe Menosky explained, "Brannon [Braga] and I went to Rick Berman's house for Thanksgiving dinner, and Brent Spiner and John de Lancie were there [....] John had an idea for a Q episode. He had a couple of interesting images, of Q on an ocean somewhere on a beach, either having lost his complete identity as Q, or lost his will to live. Somehow he gets involved with an everyday kind of person, and that person's fate and life somehow affects Q. That was his pitch, and it had some nice images." (Cinefantastique, Vol. 31, No. 11, p. 51) This not-developed story idea influentially sparked the writing of the fifth season Voyager episode "11:59". The story is similar to some elements in de Lancie's later novel, I, Q.
In the September 1999 issue of Star Trek: The Magazine, Garrett Wang reported a rumor he'd heard of a possible Kim-focused story similar to Quantum Leap. "There was an idea that I heard about, which they affectionately called around the office the Quantum Kim episode, similar to the show Quantum Leap. They were talking about that at the beginning of this season, for the end of the season, but I think after "Timeless" they wanted to save a show of that magnitude for the next season... it's a Fugitive kind of thing, the Harrison Ford thing, the wrongly accused fugitive who ends up having to become the action hero." (Star Trek: The Magazine Volume 1, Issue 5, p. 18)
Siamese twins story
Mike W. Barr devised a story for submission to Star Trek: Voyager. He later explained, "I had had the idea of Siamese twins conjoined at the spine for some time before I first utilized it as a plot pitched to the producers of Star Trek: Voyager, which was rejected." Barr later reused the story idea in his novel Gemini. (Voyages of Imagination, p. 136)
"The Terminator drone"
In the process that ultimately lead to him writing "Drone", Harry "Doc" Kloor pitched several other stories. The filmed episode evolved from a very different pitch, called "The Terminator drone". It involved Seven of Nine's nanoprobes infecting the holo-emitter, creating a killer drone. This was further modified and became "Drone". 
Tom Paris story
In the process that ultimately lead to him writing "Drone", Harry "Doc" Kloor pitched several others. His first idea had Tom Paris crashing on an alien planet, his arm almost completely ripped off. A character from an advanced race present on the planet then re-attaches the arm with Borg technology. The idea was rejected as too gory. 
In an early season 7 interview, Biller noted a concept was in the early stages of development (though never produced,) in which Voyager would introduce periods of live communication with Earth (as was introduced in "Author, Author") and "Tuvok may get a call from his daughter, from whom he is somewhat estranged. She's a little rebellious for a Vulcan, and she needs his help solving a mystery." (Star Trek: The Magazine Volume 1, Issue 20, p. 23)
Universal translator story
One of the stories Mike Sussman read during his internship involved a malfunctioning universal translator. "There was some kind of space anomaly and it turned out that everyone on the ship was actually speaking their own native language all along, like Tuvok was always speaking Vulcan and I guess Chakotay was speaking some Native American tongue. And because the universal translator was also offline, nobody could talk to each other any more," Mike Sussman stated, with a laugh. However, he also commented, "Maybe it would have made a good episode." 
Visit to a small planet
About two years before the release of Galaxy Quest, Jack Treviño and Toni Marberry pitched this story in which the crew came upon a planet that had been observing their lives on Voyager for the last three years, and on which everyone was dressed as members of the crew. As such, the crew are forced to see themselves through alien eyes. The writers felt that the fans would not accept the show having fun at their expense.  In some elements, this premise is similar to "Muse", "Blink of an Eye", and "Virtuoso".
"Who's Killing the Great Voyagers of the Delta Quadrant?"
During the show's sixth season, Bryan Fuller, a fan of alternate timelines and mirror universes, came up with an episode concept he nicknamed "Who's Killing the Great Voyagers of the Delta Quadrant?", the title being a pun on the film Who Is Killing the Great Chefs of Europe?.
Fuller described the story as:
"(...) we'd follow the crews of several alternate Voyagers. There was a Klingon crew with a "Mistress Jan'toch" – Captain Janeway in Klingon make-up – that was native to a universe where the Klingon Empire conquered the Federation two hundred years ago, a holographic crew that was essentially The Doctor to the infinite power, and several others. In each of these instances, some unseen force would destroy the alternate Voyager and its crew. Ultimately, the real Captain Janeway and her posse would discover that another alternate Voyager with a twisted Chakotay in command was responsible. He was from a universe where the Maquis overthrew the Starfleet crew. He had a personal vendetta against Janeway and Voyager, and wouldn't stop until he had snuffed each and every one of them out of existence. It was a fun, broad concept and for a brief time there seemed like a possibility that we might do it, but ultimately it never came to pass."