So last night I was collecting TOS quotes and cherry-picking whatever I could for use in my ST chronology (It really is amazing how almost every episode of TOS gives you some hint about the wider Trek universe that it's fun to decode), and I came across this well-known exchange from "Tomorrow Is Yesterday":
So I thought it might be fun to try to come up with a list of the various starships mentioned over the course of the series and try to figure out which ones were active during the time of TOS. I made a couple of general assumptions first, though.
1) I decided to limit my list to 12 total, as that's the figure they used in The Making of Star Trek, and I figure creator intent settles the "12 or 13?" question pretty well. Besides, having 13 starships in your fleet is just ASKING for trouble, and it seems that Starfleet is unlucky enough as it is.
2) I'm limiting myself to Constitution class, as that configuration seems to be what TOS considered to be a starship. IIRC, I don't think that TOS-R threw in any other types of starships in the new effects shots. I have a second list of possible other classes floating around, but on the whole I consider Starfleet to be much smaller than what we see in the TNG 24th century era.
3) Starships only, so this lets out stuff like the SS Columbia ("The Cage" / "The Menagerie"), the Antares ("Charlie X") and the SS Beagle ("Bread and Circuses").
Here's what I came up with (You can ignore the years, as those relate to my own Trek timeline):
12 Constitution-class Starships (Active during the 5YM):
1) USS Enterprise (NCC-1701) – Commanded by Captain James T. Kirk
Shuttlecraft Columbus (NCC-1701/2), Einstein (NCC-1701/6), Galileo (NCC-1701/7)
2) USS Constellation (NCC-1017) – Commanded by Commodore Matthew Decker, Destroyed by the planet-killer in 2268 (“The Doomsday Machine”)
3) USS Yorktown (NCC-1717) – Commanded by the former “Number One” in John Byrne’s Trek comics (mentioned in “Obsession”)
4) USS Intrepid (NCC-1631) – Manned entirely by Vulcans, Destroyed in 2269 (“Court Martial”, “The Immunity Syndrome”)
5) USS Lexington (NCC-1709) – Commanded by Commodore Robert Wesley, Lt. Watley transfers to Enterprise (“The Ultimate Computer”, DS9: “Trials and Tribble-ations”)
6) USS Excalibur (NCC-1664) – Commanded by Captain Harris (I’ll say that the unseen Captain Harris should preferably be a woman, because God knows we’ve got no shortage of WASP male Captains in TOS), Severely damaged, all personnel killed in 2269 M-5 incident (“The Ultimate Computer”)
7) USS Hood (NCC-1703)– Damaged in 2269 M-5 incident (“The Ultimate Computer”)
8) USS Potemkin (NCC-1657) – Damaged in 2269 M-5 incident (“The Ultimate Computer”, “Tunabout Intruder”)
9) USS Exeter (NCC-1672) – Commanded by Captain Ronald Tracey, Crew killed by bacteria at Omega IV in 2269 (“The Omega Glory”)
10) USS Defiant (NCC-1764) – Commanded by Caucasian Male Human Captain, Disappears in interspace (“The Tholian Web”, “In a Mirror, Darkly”)
11) ?
12) ?
Starfleet Captains with unknown ships: Captain Krasnovsky (blue shirt, possibly commander of the Intrepid, before it switched over to the all-Vulcan crew?), Captain Chandra (both seen at Starbase 11 in “Court Martial”) Garth of Izar (commanding the USS Heisenberg according to the Garth of Izar novel)
Space Command Captain Lindstrom (seen at Starbase 11 in “Court Martial”, probably not a starship commander from that title)
Older Starships (Likely decommissioned or destroyed by the time of the 5YM)
1) USS Horizon (Daedalus class, NCC-176) – Destroyed shortly after visiting Sigma Iotia II in 2169 (“A Piece of the Action”)
2) USS Archon (Daedalus class, NCC-189) – Disappeared after visiting Beta III in 2167 (“Return of the Archons”)
3) USS Constitution (Constitution class, NCC-1700)
4) USS Republic (Constitution class, NCC-1371) – Commanded by Captain Garrovick, Ensign Ben Finney, Ensign James T. Kirk (“Court Martial”)
5) USS Farragut (Constitution class, NCC-1647) – Commanded by Captain Garrovick, Assistant Engineer James T. Kirk – Half of the crew killed in 2257 (“Obsession”)
6) USS Valiant (NCC-1223) – Destroyed after being declared a causality in the war between Eminiar VII and its neighboring planet Vendikar in 2217 (“A Taste of Armageddon”)
7) USS Kelvin (Kelvin class, NCC-0514) – Commanded by Captain Richard Robau, First Officer Lt. Commander George Kirk (I presume it likely that it existed in the Prime timeline in some form, but it successfully completed its mission and was decommissioned instead of destroyed)
Conjectural Starships in the TOS era (other classes) - List compiled by the highly scientific method of "Having names that I like"
1) USS Reliant (Miranda class, NCC-1864) – Commanded by Captain Clark Terrell (Star Trek II: The Wrath of Khan)
2) USS Grissom (Oberth class, NCC-638) – Commanded by Captain Esteban (Star Trek III: The Search For Spock)
3) USS Bozeman (Soyuz class, NCC-1941) – Commanded by Captain Morgan Bateson, Disappeared in 2278 (TNG: “Cause and Effect”)
4) USS Saratoga (Miranda class, NCC-1937) – Disabled by alien probe in 2284 (Star Trek IV: The Voyage Home)
5) USS El Dorado (NCC-1722) – Mixed alien crew, First Officer James T. Kirk (Star Trek II Biographies)
6) USS Saladin (Saladin class destroyer, NCC-500) – Commanded by Commander James T. Kirk (Star Trek II Biographies)
7) USS Sirius (NCC-1744) – Assistant Science Officer Spock (Star Trek II Biographies)
8) USS Phardos (NCC-1757) – Science Officer Spock (Star Trek II Biographies)
9) USS Artemis – Third Officer and Science Officer Spock (Vulcan’s Glory)
10) USS Columbia
11) USS Discovery (NCC-1031) (Hey, we have to fit this sucker in here somewhere)
12) USS Kongo (NCC-1710, Constitution class)
13) USS Hornet
14) USS Wasp
15) USS Lafayette (NCC-1720) – Chief Medical Officer Leonard McCoy (Star Trek II Biographies)
16) USS Argo
17) USS Nautilus
18) USS Pegasus
19) USS Olympia
20) USS Oberth (NCC-602) – Potential participant in Operation Retrieve (Star Trek VI: The Undiscovered Country)
21) USS Eagle (NCC-956) – Potential participant in Operation Retrieve (Star Trek VI: The Undiscovered Country)
22) USS Endeavor (NCC-1895, Constitution class) – Potential participant in Operation Retrieve (Star Trek VI: The Undiscovered Country)
23) USS Venture
CHRISTOPHER: Must have taken quite a lot to build a ship like this.
KIRK: There are only twelve like it in the fleet.
CHRISTOPHER: I see. Did the Navy--
KIRK: We're a combined service, Captain. Our authority is the United Earth Space Probe Agency.
So I thought it might be fun to try to come up with a list of the various starships mentioned over the course of the series and try to figure out which ones were active during the time of TOS. I made a couple of general assumptions first, though.
1) I decided to limit my list to 12 total, as that's the figure they used in The Making of Star Trek, and I figure creator intent settles the "12 or 13?" question pretty well. Besides, having 13 starships in your fleet is just ASKING for trouble, and it seems that Starfleet is unlucky enough as it is.
2) I'm limiting myself to Constitution class, as that configuration seems to be what TOS considered to be a starship. IIRC, I don't think that TOS-R threw in any other types of starships in the new effects shots. I have a second list of possible other classes floating around, but on the whole I consider Starfleet to be much smaller than what we see in the TNG 24th century era.
3) Starships only, so this lets out stuff like the SS Columbia ("The Cage" / "The Menagerie"), the Antares ("Charlie X") and the SS Beagle ("Bread and Circuses").
Here's what I came up with (You can ignore the years, as those relate to my own Trek timeline):
12 Constitution-class Starships (Active during the 5YM):
1) USS Enterprise (NCC-1701) – Commanded by Captain James T. Kirk
Shuttlecraft Columbus (NCC-1701/2), Einstein (NCC-1701/6), Galileo (NCC-1701/7)
2) USS Constellation (NCC-1017) – Commanded by Commodore Matthew Decker, Destroyed by the planet-killer in 2268 (“The Doomsday Machine”)
3) USS Yorktown (NCC-1717) – Commanded by the former “Number One” in John Byrne’s Trek comics (mentioned in “Obsession”)
4) USS Intrepid (NCC-1631) – Manned entirely by Vulcans, Destroyed in 2269 (“Court Martial”, “The Immunity Syndrome”)
5) USS Lexington (NCC-1709) – Commanded by Commodore Robert Wesley, Lt. Watley transfers to Enterprise (“The Ultimate Computer”, DS9: “Trials and Tribble-ations”)
6) USS Excalibur (NCC-1664) – Commanded by Captain Harris (I’ll say that the unseen Captain Harris should preferably be a woman, because God knows we’ve got no shortage of WASP male Captains in TOS), Severely damaged, all personnel killed in 2269 M-5 incident (“The Ultimate Computer”)
7) USS Hood (NCC-1703)– Damaged in 2269 M-5 incident (“The Ultimate Computer”)
8) USS Potemkin (NCC-1657) – Damaged in 2269 M-5 incident (“The Ultimate Computer”, “Tunabout Intruder”)
9) USS Exeter (NCC-1672) – Commanded by Captain Ronald Tracey, Crew killed by bacteria at Omega IV in 2269 (“The Omega Glory”)
10) USS Defiant (NCC-1764) – Commanded by Caucasian Male Human Captain, Disappears in interspace (“The Tholian Web”, “In a Mirror, Darkly”)
11) ?
12) ?
Starfleet Captains with unknown ships: Captain Krasnovsky (blue shirt, possibly commander of the Intrepid, before it switched over to the all-Vulcan crew?), Captain Chandra (both seen at Starbase 11 in “Court Martial”) Garth of Izar (commanding the USS Heisenberg according to the Garth of Izar novel)
Space Command Captain Lindstrom (seen at Starbase 11 in “Court Martial”, probably not a starship commander from that title)
Older Starships (Likely decommissioned or destroyed by the time of the 5YM)
1) USS Horizon (Daedalus class, NCC-176) – Destroyed shortly after visiting Sigma Iotia II in 2169 (“A Piece of the Action”)
2) USS Archon (Daedalus class, NCC-189) – Disappeared after visiting Beta III in 2167 (“Return of the Archons”)
3) USS Constitution (Constitution class, NCC-1700)
4) USS Republic (Constitution class, NCC-1371) – Commanded by Captain Garrovick, Ensign Ben Finney, Ensign James T. Kirk (“Court Martial”)
5) USS Farragut (Constitution class, NCC-1647) – Commanded by Captain Garrovick, Assistant Engineer James T. Kirk – Half of the crew killed in 2257 (“Obsession”)
6) USS Valiant (NCC-1223) – Destroyed after being declared a causality in the war between Eminiar VII and its neighboring planet Vendikar in 2217 (“A Taste of Armageddon”)
7) USS Kelvin (Kelvin class, NCC-0514) – Commanded by Captain Richard Robau, First Officer Lt. Commander George Kirk (I presume it likely that it existed in the Prime timeline in some form, but it successfully completed its mission and was decommissioned instead of destroyed)
Conjectural Starships in the TOS era (other classes) - List compiled by the highly scientific method of "Having names that I like"

1) USS Reliant (Miranda class, NCC-1864) – Commanded by Captain Clark Terrell (Star Trek II: The Wrath of Khan)
2) USS Grissom (Oberth class, NCC-638) – Commanded by Captain Esteban (Star Trek III: The Search For Spock)
3) USS Bozeman (Soyuz class, NCC-1941) – Commanded by Captain Morgan Bateson, Disappeared in 2278 (TNG: “Cause and Effect”)
4) USS Saratoga (Miranda class, NCC-1937) – Disabled by alien probe in 2284 (Star Trek IV: The Voyage Home)
5) USS El Dorado (NCC-1722) – Mixed alien crew, First Officer James T. Kirk (Star Trek II Biographies)
6) USS Saladin (Saladin class destroyer, NCC-500) – Commanded by Commander James T. Kirk (Star Trek II Biographies)
7) USS Sirius (NCC-1744) – Assistant Science Officer Spock (Star Trek II Biographies)
8) USS Phardos (NCC-1757) – Science Officer Spock (Star Trek II Biographies)
9) USS Artemis – Third Officer and Science Officer Spock (Vulcan’s Glory)
10) USS Columbia
11) USS Discovery (NCC-1031) (Hey, we have to fit this sucker in here somewhere)
12) USS Kongo (NCC-1710, Constitution class)
13) USS Hornet
14) USS Wasp
15) USS Lafayette (NCC-1720) – Chief Medical Officer Leonard McCoy (Star Trek II Biographies)
16) USS Argo
17) USS Nautilus
18) USS Pegasus
19) USS Olympia
20) USS Oberth (NCC-602) – Potential participant in Operation Retrieve (Star Trek VI: The Undiscovered Country)
21) USS Eagle (NCC-956) – Potential participant in Operation Retrieve (Star Trek VI: The Undiscovered Country)
22) USS Endeavor (NCC-1895, Constitution class) – Potential participant in Operation Retrieve (Star Trek VI: The Undiscovered Country)
23) USS Venture
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