These of some of the ones I found......everyone feel free to add you own requests.
This Challenger-class seem to originate with a 1992 TNG comic entitled "Thin Ice" which depicted a supposedly Challenger-class U.S.S. Marco Polo, although the appearance of the ship in the comic is quite different from the schematic of the fan-envisioned deisgn.
http://www.battleclinic.com/docks/files/dist/index.php/file,6d03cdfb7d8ac08ae0974dca56a99d1f.zipClaymore,U.S.S.
Federation starship, operated under the authority of Starfleet Intelligence. This ship is a four-deck scout, but has a large sensor plate for long range emissions testing and information interception. (Star Fleet Intelligence--Agent's Orientation Sourcebook [FASA RPG]).
Baker, U.S.S.
Federation starship, prototype for the Baker-class destroyer. (Federation Starship Recognition Manual [FASA RPG]).
B'tly, U.S.S.
Federation starship, Decker-class heavy destroyer, Starfleet registry NCC-6037. Named for Irkin B'tly. Built in 2348, the B'tly went missing in 2363. (FASA Officer's Manual [TNG]).
Daran, U.S.S.
Federation starship, Daran-class fast frigate, Starfleet registry NCC-3201. The Daran was built by Aria Mastac's Prime Dockyards on Daran V, the first vessel of its class. The keel was laid down on stardate 5915.3, and the vessel was launched on 6075.1 and commissioned on 6108.73. The Daran was one of four starships that faced the fleet of the bounty hunter Sweeney in a 2288 battle over Tau Gamma II, along with the Avenger, Enterprise-A and Exeter. ("Going, Going..." [DC TOS vol.2 #8; "... Gone!" [DC TOS vol.2 #9]; Ships of the Star Fleet).
Elkins, U.S.S.
Federation starship, Starfleet registry NCC-74121. The Elkins was one of the vessels that fought in the Dominion War. (Technical Manual [DS9]). A photo of this ship reveals it is comprised of a modified Intrepid model with Constitution refit nacelles, Danube runabout nacelle pylons and, shockingly enough, either a backwards Star Wars A-Wing or an F-16 as the secondary hull. The ship was apparently named for DS9 staffer Judy Elkins, and used in background fleet scenes during Dominion War story arcs. This photo is a corrected modification of the Technical Manual picture, edited by Bernd Schneider of Ex Astris Scientia.
Mann-class.
Type of Federation starship used in the 2220s. The Klingon Empire called this class 'hokot' in intelligence reports. Ships built of this design include the Poseidon, Endurance and of course, the Mann . ("The Final Reflection" [Pocket TOS]).
Columbia, U.S.S.
Federation starship, Cygnus-class scout, Starfleet registry NCC-621. Second starship to bear the name. The construction of this vessel was authorized by an appropriation of Mk-VIIB scouts on stardate 5099. The Columbia was ordered by Commodore Probert to rendezvous with the starship Revere on stardate 7412. ("The Motion Picture" [Movie #1]; Technical Manual [TOS]; Federation Starship Recognition Chart).
Cousteau.
The captain's yacht docked on the starship Enterprise-E. Captain Picard illegally detached this vessel in 2374 in order to ferry equipment to the Ba'ku to help them defend themselves from a So'na invasion that was supported by a Starfleet admiral. ("Insurrection" [Movie #9]).
Abrams, U.S.S.
Federation starship, Hardin-class heavy cruiser, Starfleet registry NCC-8001. Built on Argelius II in 2330. (FASA Officer's Manual [TNG]).
Abu Bekr, U.S.S.
Federation starship, Cochise-class destroyer, Starfleet registry NCC-549. (Technical Manual [Franz Joseph TOS]).
Adams, U.S.S.
Federation starship, Dollond-class transport/tug, Starfleet registry NCC-3925. (Technical Manual [Franz Joseph TOS]).
Adjuvant, U.S.S.
Federation starship, Ariel-class shuttlecarrier, Starfleet registry NCC-2202. (Ships of the Star Fleet [Mastercom]).
Albert Einstein.
Shuttlecraft 02 on the starship Enterprise-D. The Einstein was dragged into a wormhole while en route to Beta Hydros IV and deposited in the Delta Quadrant in 2367. The crew of the shuttle was stranded in a alien junkyard until they managed to use a derelict transwarp vessel to propel themselves home. ("The Flight of the Albert Einstein" [DC TNG vol.2 #20]; "Mourning Star" [DC TNG vol.2 #21]; "Trapped" [DC TNG vol.2 #22]; "The Barrier" [DC TNG vol.2 #23]; "Homecoming" [DC TNG vol.2 #24]).
Amalthea Rex, U.S.S.
Federation starship, Brande-class frigate, Starfleet registry NCC-9003. The Amalthea Rex was built by Starfleet in 2291 at Gibraltar on Terra. (Officer's Manual [FASA TNG]).
Argo.
Shuttle used aboard the starship Enterprise-E. The Argo is a large carrier used to transport heavy equipment to a planet's surface. In 2378 it was used to transport a ground vehicle that was to be used by Picard, Worf and Data to the surface of a planet. ("Nemesis" [Movie #10]).
Nomad.
Terran space probe launched in 2002. ("The Changeling" [TOS]).
Pytheas-class.
Type of Federation starship. (Federation Starship Recognition Chart).
Robert Fox, S.S.
Civilian space vessel, a Whorfin-class transport. The Robert Fox, named for a famous Federation diplomat, was carrying El-Aurian refugees in 2293 when it became ensnared in the Nexus and destroyed. ("Generations" [Movie #7]).
Romulan Warbird A This one is my favorite
Spartan, U.S.S.
Federation starship, Caracal-class cruiser, Starfleet registry NCC-752. The Spartan's keel was laid down on 11 July 2181, and the vessel was launched on 4 February 2184 and commissioned on 5 October, that year. This vessel was decommissioned on 29 April 2230, and scrapped the next year.
Sphinx, U.S.S.
Federation starship, a Centaurus-class courier, commanded by Jack Casden. ("Cloak" [Pocket TOS Section 31]).
Valiant, S.S.
Early interstellar exploration vessel that was lost at the Galactic Barrier in 2065. Shortly after contact with the barrier, at least one crew member mutated into a godlike being, forcing the ship’s captain to order the Valiant destroyed to prevent the escape of the mutated crew member. ("Where No Man Has Gone Before" [TOS #1]; "Valiant" [Pocket TNG]).
Valiant, U.S.S.
Federation starship, Royal Sovereign-class strike cruiser, Starfleet registry NCC-3010. The sixth Federation starship known to bear this name. (Officer's Manual [FASA TNG RPG]).
Well that's a start lol
-MP