Well with so many to choose from it's hard to come up with a "definative" list... That said however, most of the time I'm using the following....
BattlecruisersTOS: I have a self made bash using Lord Shctupps DN and DD models
TMP: Mainly the Rogue9 variants (P-81 based) and the P-81 Excelsior
BattleshipsTOS: Desty Nova's Mars, Lord Schtupps Mars (when he releases it of course...
) and Stress Puppy's Yamato
TMP: Mackie's P-81 based Einherjer and WZ's Mars Refit
Lord Schutpp's Galaxy sot of sits between eras so I'v added a seperate shiplist enty for that
CarriersTOS: Anduril's Julius Ceasar and Atrahasis' Coronado
TMP: WZ's Ark Royal and Audacity, P-81's George "Dubya" Bush, Rogue9's Oriskany and Anarion's Churchill
CruisersTOS: Lord Schtupp's Connie, Stress Puppy's Connie and all of Atrahasis' TOS SOTF variants
TMP: P-81's Connie, WZ's Connie, Mackie's Ironcross, DTW's P-81 based Belknap, Ticonderoga and Tikopai, and all off Atrahasis SOTF TMP refits
DestroyersTOS: All of Lord Schtupp's single nacelle variants plus Atrahasis' Saladin and Sivo
TMP: P-81's Abbe and Akula plus Rogue9's P-81 Remora
DreadnoughtsTOS: Lord Schtupp's and Anduril's Federation
TMP: P-81 Star Empire and Star League, WZ's Federation and Belicose
FrigatesTOS: Atrahasis' Aurora, Burke and Kearsage
TMP: DTW's P-81 based Okinawa and WZ's Okinawa
Light CruisersTOS: Atrahasis' SOTF variants and Lord Schtupp's Surya
TMP: Rogue9's P-81 Miranda variants Mackie's P-81 based Davids
I also use the Rogue9 P-81 based Loknars and Larson, Pataflafla's Northampton and Kiev and all the "X-tech" P-81 models. Have just added Terradyne's Spectre and "Tugs and Freighters" are provided by Lord Schtupp and WZ. I use my own Chandleys (of course...
) and they have their own "Light Cruiser" entry in the shiplist, as do a lot of the FASA ships as their classifications differ from SFC's.
I've also added entries to the ship list to cover things that aren't already in there and deserve a seperate enty. These include standalone entries for the ships seen in TOS/TMP which I suppose I class as "Legends" (Enterprise, Excelsior, Reliant etc) and by removing them from the strings and shipname files stops them accidentally appearing again. The trouble with this of course is that I have 12 different Enterprises so I usually rotate between the Khaliban 1701, the Wicked Zombie 1701 and the P-81 1701 for TMP and the Lord Schtupp and Anduril 1701 for TOS. Nobody has yet done a high res/poly Reliant yet so the P-81 one gets used and I always use the P-81 Excelsior (standard and Enterprise - B refit)
Not an exhaustive list by no means plus, I'll have forgotten loads of models that I've added....
Anyway, there you go