This may not be entirely accurate, as I'm writing it from my desk at work rather than at home where I have manuals and notes and so forth. I may well be forgetting some very important facts -- lets get a dialogue going regarding this list...
Wing Commander:
Hornet class Light Fighter (?)
CF-105 Scimitar class Medium Fighter (2526*)
Rapier II class Medium Fighter (2654)
Raptor class Heavy Fighter (2639*)
Wing Commander II:
P-64 Ferret class Patrol Fighter (2639*)
F-54 Epee class Light Attack Fighter (2654*)
F-57 Sabre class Heavy Attack Fighter (2634*)
A-10 Broadsword class Heavy Bomber (2648)
Wraith class Medium Fighter (2667)
Wing Commander III:
Arrow V class Light Fighter (2654*)
F-86 Hellcat V class Medium Fighter (2654*)
F-66 Thunderbolt VII class Heavy Fighter (2668)
F/A-76 Longbow class Heavy Fighter (2654*)
F-103 Excalibur class Heavy Space/Atmospheric Fighter/Bomber (2669)
Wing Commander IV:
F-104 Bearcat class Heavy Fighter (2673)
F-107 Lance class Heavy Fighter (2672)
Armada:
Phantom (?)
Gladius (?)
Banshee (?)
Wing Commander Prophecy:
F/A-105 Tigershark class Multi-Role Fighter (?)
F-106 Piranha class Scout Fighter (?)
F-108 Panther class Space Superiority Fighter (?)
F-109 Vampire class Space Superiority Fighter (?)
F-110 Wasp class Interceptor (?)
TB-80 Devestator class Torpedo Bomber (?)
TB-81 Shrike class Torpedo Bomber (?)
A few technical commentaries...
An asterix marks the first time a ship has been known to be in service. No asterix means a specific service entry date. A question mark means we've only seen said ship referenced as early as whatever game it appears in (Prophecy ships all first appear in 2681, Armada ships 2668, so forth).
The Phantom and the Gladius seem to be developments of the Raptor class ships.
There is an interesting theory regarding the Hellcat and its appearince in WCA (giving it the 2654 date) -- it has been suggested that this may be its predecessor, the Action Stations' era *Wildcat*... which would explain the Hellcat statue at the Academy grounds. I'm definately in favor of this, although it's not directly supported anywhere.