(written from a Production point of view)
The Case of Jonathan Doe Starship was an article about starship registries, published in the fanzine T-Negative Nr. 27 of April, 1975 and written by Greg Jein as a "Trekkie", long before he became an official, long-serving, Star Trek studio model builder.
The article had apparently been circulating among fans for some time prior to that date, as it was sent in to the magazine by several people, including Jein himself, as a response to a reader question in an earlier issue of the magazine. With most of its contents adopted and elevated into canon by the Star Trek franchise, Jein's article became one of the very few, but most influential nonetheless, pieces of "fan fiction", to be adopted by the official franchise.
Determining starship registries
In the article, Jein attempted to create a list of starships with their respective registry numbers. Since no such lists existed at the time, he chose to use the registries seen in the first season episode "Court Martial" of Star Trek: The Original Series as a basis for his list. However, as he explained, he "combined confusion, circumstance, and innuendo to produce illogic, but it relatively (in the loosest possible sense) forms a semi-cohesive pattern."
He then claimed that the Constellation, Defiant, Farragut, Kongo, Republic and Valiant were unlikely to have appeared on the Starbase 11 chart, due to them being either not yet constructed or no longer in active service. Removing these ships left twelve, exactly the number of starships mentioned by Kirk in the first season episode "Tomorrow is Yesterday".
Jein then matched these 12 names to the 10 numbers on the chart by using a reverse alphabetical ordering, arriving at the following matches:
|NCC number||Starship name|
- The actual chart seems to read NCC-1831, but Greg Jein may have misread it as 1631, unsurprisingly perhaps, as he had to make do with a low-resolution still (given to him by future Star Trek reference author, but fan at the time, Kay Anderson) from the already low-resolution original run of the series. As Michael Okuda had access to an early 1990s remastered version of the episode at the time, he corrected this number in his registry list, otherwise largely based on Jein's, in his first 1994 edition of the Encyclopedia to 1831 (though he had overlooked to change the individual entry for Intrepid accordingly). Nevertheless, Okuda re-corrected himself in the third 1999 edition and applied the original 1631 intent in the 2006-2008 remastered version of the Original Series. It was exactly for this reason why Matt Jefferies avoided the numbers 6 and 8 when he devised the original registry number for the Enterprise. (Star Trek: The Original Series Sketchbook, p. 62)
Although he himself admitted there was little logical reasoning behind this ordering, it did lead by chance to several interesting matches. The 1701 was correctly assigned to the Enterprise, and the 1700 was very conveniently matched to the USS Constitution, the presumed first ship of the Constitution-class. Furthermore, the Intrepid had the longest bar on the chart, perhaps indicating it had finished repairs, as the plot for "Court Martial" suggested. Incidentally, Jein's observation of a "Constitution-class" struck a cord with production staffers and fans alike, and it was "understood" to have established the Enterprise and her sisters belonging to the Constitution-class ever since, thereby replacing the somewhat non-committal "Starship-class" designation, even though a conformational canon reference had to wait until 1982.
In conclusion, Greg Jein presented a "projected list" of starships, each accompanied with a registry number with names and classifications not seen in "Court Martial", as well as including one vessel never mentioned before (or later for that matter) in any official works or production sources. The names not established in the series proper, he took from the three lists Writer/Story Editor D.C. Fontana and Producer Robert Justman proposed at the start of the production of the second season of The Original Series, which included the final fourteen-name one (see: Constitution-class: Footnotes). Registry numbers not featured in the series, Jein made up, taking care to have them correspond with the classification numbering. This included the one for the USS Defiant as that name was not yet foreseen by the producers when they composed their lists. Due to its late on-screen appearance in the series, Jein reasoned that it must have been a very recent addition to the class, so he gave it the fourth highest registry number, one he made up. According to Jein, this implied that Defiant, commissioned somewhere during the TOS era, therefore had an unfortunately short career, at least in Star Trek's prime universe, or as Jein had succinctly put it in his article, "Tough break". The single unreferenced ship, the USS Tashik-Sotra, was an acknowledgment of Justman's annotation on his proposal of 9 August 1967, where the latter remarked, "In addition, I think a name ought to be made up that would be of Vulcan origin." While not adopted, some of Justman's notion was carried over to having the Intrepid a crew that was almost entirely composed of Vulcans. (The Making of Star Trek, pp. 164-165)
|NCC number||Starship name||Class|
|NCC-1700||USS Constitution||Mk. IX deep space cruiser|
|NCC-1017||USS Constellation||Mk. VII interstellar cruiser|
|NCC-1764||USS Defiant||Mk. IX deep space cruiser|
|NCC-1685||USS Eagle||Mk. VIII interstellar cruiser|
|NCC-1719||USS Endeavor||Mk. IX deep space cruiser|
|NCC-1701||USS Enterprise||Mk. IX deep space cruiser|
|NCC-1697||USS Essex||Mk. VIII interstellar cruiser|
|NCC-1664||USS Excalibur||Mk. VIII interstellar cruiser|
|NCC-1672||USS Exeter||Mk. VIII interstellar cruiser|
|NCC-1647||USS Farragut||Mk. VIII space cruiser|
|NCC-1703||USS Hood||Mk. IX deep space cruiser|
|NCC-1868||USS Hornet||Mk. X deep space cruiser|
|NCC-1631||USS Intrepid||Mk. VII interstellar cruiser|
|NCC-1732||USS Kongo||Mk. IX deep space cruiser|
|NCC-1866||USS Lafayette||Mk. X deep space cruiser|
|NCC-1709||USS Lexington||Mk. IX deep space cruiser|
|NCC-1702||USS Potemkin||Mk. IX deep space cruiser|
|NCC-1371||USS Republic||Mk. VI space cruiser|
|NCC-1865||USS Tashik-Sotra||Mk. X deep space cruiser|
|NCC-1623||USS Valiant||Mk. VII interstellar cruiser|
|NCC-1717||USS Yorktown||Mk. IX deep space cruiser|
The classification of these ships was based on information from a technical diagram labeled 'Primary Phaser L, R', constructed for the script requirements of the first season episode "Space Seed", but only seen very briefly and partially in the later season two episode "The Trouble with Tribbles". The graphic was actually created by Art Director Matt Jefferies, who used his own extensive aviation library as his source. Depicted were two varieties of hydraulic fluid reservoirs, used by the US Air Force at the time.  The diagram was endowed with a caption, gleaned by Jein for his article after he had obtained a trimmed clipping from Lincoln Enterprises showing the graphic in its entirety, that read:
PRIMARY PHASER L, R STAR SHIP MK IX/01 CONSTITUTION CLASS
Taking his cue from the "MK IX/01" specifier from the graphic caption, Jein postulated that this was a newer design variant, or sub-class, with the Constitution being the first, prototype MK IX (sub-)class vessel with the Enterprise as it second member, hence the "01" addition to both the registry "NCC-17" and the technical journal graphic as seen. The vessels with lower registry numbers he assigned lower variant class specifiers accordingly, though he had made an error with the Constellation (having it switched with that of the Republic would have made his list entirely consistent). As he had already established that the producers of the Original Series proceeded from a class launch in the mid-2220s (The Making of Star Trek, p. 203), much older Constitutions with a lower registry number could have existed, being either destroyed or decommissioned prior to 2245, the by the production staff generally accepted – though not firmly confirmed – launch year of the Enterprise. Noteworthy was, that the original designer of the Enterprise and its registry number, Matt Jefferies, has endorsed the rationale behind Jein's numbering system to some extent, "The reason we gave for the choice [NCC-1701] afterwards was that the "Enterprise" was the 17th major design of the Federation, and the first in the series. 17-01!" (Star Trek: The Original Series Sketchbook, p. 62),
The class variations in the diagram featured on the right may or may not have an exact similar appearance to the Enterprise.
Acceptance of Greg Jein's numbers
These registry numbers, and in some cases, the ships in this list that were not actually seen on Star Trek, have made their way into official works. The first major adoptions of these numbers were in Bjo Trimble's first commercial 1977 reference book edition of the Star Trek Concordance and in the FASA role-playing game of the early-to-mid 1980s, both of which, as licensed products, considered "official" at the time.
In the 1990s, licensed, and to date still by the Star Trek franchise maintained as official, reference works by Michael Okuda in particular, most notably his Star Trek Encyclopedia, started using these numbers as a tip-of-the-hat to Greg Jein who had become the regular studio model vendor for Star Trek: The Next Generation by that time (ànd who had provided Okuda himself with reference models for representation in his Star Trek Chronology to fill in gaps in Star Trek history), as Okuda himself stated on a later occasion, "I might note that some of the ship registry numbers came from Greg Jein's interpretation of the starship chart in Commodore Stone's office in "Shore Leave" (TOS) [sic; The actual episode with Commodore Stone is "Court Martial", not "Shore Leave"]." 
Despite being non-canon at the time, producers did seem to regard these numbers as the official ones for their respective ships. This was emphasized by Mike Okuda himself, as he specifically mentioned Jein's article as the only non-official, outside production reference source (and a fan-produced one at that) in the official Encyclopedia (3rd ed., pp 85-86), without acknowledging or using any other. The 2006 remastered episode versions of The Original Series featured several of the original vessels with visible registry numbers, which had previously been indiscernible in their original appearances – not being there at all actually – , and they were all based on the list as it was published in the Encyclopedia. Where applicable in the remastered series, Visual Effects Supervisor Okuda made use of the opportunity to marry Jein's numbers to their respective ships.
They concerned the following vessels and their respective appearances:
- USS Defiant (NCC-1764) in ENT: "In a Mirror, Darkly" and TOS-R: "The Tholian Web"
- USS Exeter (NCC-1672) in TOS-R: "The Omega Glory"
- USS Intrepid (NCC-1631) in TOS-R: "Court Martial"
- USS Excalibur (NCC-1664) in TOS-R: "The Ultimate Computer"
- USS Hood (NCC-1703) in TOS-R: "The Ultimate Computer"
- USS Lexington (NCC-1709) in TOS-R: "The Ultimate Computer"
This accounted for all the visually established, unnumbered, Constitution-class vessels seen in the original run of the series – though the Intrepid was originally not featured there visually, but especially retconned into the remastered version –, save one. The conspicuous (as it was seen on-screen) exception concerned the USS Potemkin (NCC-1657) for which a made-up registry number had already been conceived by Okuda himself for representation on the Starship Mission Assignments chart and the Operation Retrieve briefing charts, seen and unseen in Star Trek VI: The Undiscovered Country. But since he had already propagated this registry in his subsequent reference works, he chose to leave the registry for the ship as is.
Where Jein's finalized list was concerned there were two additional, less conspicuous, exceptions for similar reasons; the first one concerned the USS Eagle (NCC-956), which, while being one of the original names considered by the producers, was not seen but merely referenced on one of the Undiscovered Country briefing charts. The other, even less conspicuous, case applied to the USS Kongo (NCC-1710) which was one of two Constitution-class vessels (along with the USS Constitution) not even been referenced to in the Original/Animated Series in any form or format, save for their inclusion on the original producer's final fourteen-name list, and has only been named on the Starship Mission Assignments chart in the Undiscovered Country, albeit nearly illegible. Its registry originated from the Star Fleet Technical Manual, and in this case it was for Okuda even more opportune to leave the registry as is, due to its very ephemeral reference.
Memory Alpha deemed Jein's registries/ship combinations, insofar they were not confirmed on-screen, conjectural and/or apocryphal, and not part of the established canon until the advent of the remastered series in 2006, when the retconning was effected. The ones done on that occasion at least, pursuant the early retconning for Defiant in "In a Mirror, Darkly", are as such considered elevated to canon by Memory Alpha.
A major perceived inconsistency with the scheme presented by Greg Jein is the apparent existence of ships with registry numbers lower than the number of the class ship (the Constitution's NCC-1700). Furthermore, and Jein repeatedly reminds the reader of this, the above scheme is not particularly scientific or logical, and is mostly derived from conjecture and random chance. Yet, as explained above, what Jein's detractors had at the time consistently failed to fathom was, that he actually had accounted for the numbering discrepancy.
A fan-appointed so-called "major competitor" on the subject of Constitution-class registries had previously been the above mentioned Star Fleet Technical Manual by Franz Joseph, published in 1975. In his book, Franz Joseph listed the Constitution-class starships, sometimes as member of some sub-class, with much more consistent registry numbers ranging from NCC-1700 to NCC-1843. Franz Joseph also used a variation of the 'Mk IX' classification. To add to the confusion, the Star Fleet Technical Manual was at one time also regarded as "official", just like the later FASA material. There were on screen references to the Technical Manual ships in Star Trek: The Motion Picture, with the USS Merrimack (NCC-1715) as an example of a starship with a Franz Joseph-derived registry number. For these reasons, many fans preferred Joseph's list above Jein's, resulting that there had been no clear consensus on the issue at the time. And indeed, even Okuda made use of Joseph' work for his "Operation Retrieve" charts, having stated, "Other registry numbers came from Franz Joseph's Star Fleet Technical Manual or his starship blueprints," which incidentally, included that of USS Kongo.  However, since he concurrently had made the "Jein's interpretation" remark on the very same occasion, this was a stark indication that he only had become aware of Jein's article in the time period that he was working on both the The Undiscovered Country and the Encyclopedia, and Okuda from there on end has strictly adhered to Jein's article. It was the penultimate recorded occasion that Joseph's work was ever referenced as a production source. Furthermore, Okuda's contributions to the remastered project and the formal "debunking" of Joseph's work seemed to have settled the matter once and for all. While a dwindling number of die-hard fans still adhere to the work, the official franchise has formally distanced itself from the Technical Manual, dismissing it as "unofficial" and relegating the work to apocrypha status, as it had done with every other (in-universe) reference work, prior to the Chronology. (Star Trek: The Magazine Volume 2, Issue 11, p. 71)
Apart from these two major lists, there have been a few cases in which on screen references to Constitution-class starships have ignored any of the systems. The most notable example was the USS Constellation, whose exceptionally low registry number, "NCC-1017" was the only one visually established in the original run of the Original Series. It, although introduced before any of these lists were set up, has set the precedent for starships using registry numbers lower than that of their class lead ship (in reality the decal sheet of the 1966 first edition AMT Enterprise model kit , no. S921 and from which the Constellation filming model was constructed, only contained the NCC-1701 number and the ship's number was constructed by reshuffling the one decal). The other example was the USS Potemkin, which was given the registry NCC-1657 in The Undiscovered Country, as already explained.