I get a lot of my ship names from the old Jackill's Star Fleet Reference Manual. My Odyssey trio is named Concordat, Konkordium, Concordance. All words meaning an agreement, suitable names for a front line Federation starship.
My Romulan Liberated Borg character made it to Level 30 and beat the (old) Defense of New Romulus with the skill point bug.
U.S.S. Disturbed, Tac, Mirror Assault Cruiser~Band
U.S.S. Moretsu, Eng, Galor~Anime
U.S.S. Ergo Proxy, Eng, Patrol Escort~Anime
I.K.S. Void Stalker, Tac, Bortesqu~evocative
I.K.S. Kaimetsu, Eng, Bortesqu~japanese for destruction/annihilation
I.K.S. Azure, Sci, Bortasque~Tetryon build. characters name is Sapphire, it was planned from the start
U.S.S. Azure Fury, Sci, Patrol Escort~another tetryon build, the kdf was so fun had to try a fed version.
just the final ships at present, planning on acquiring an armitage which will go to the tac, also named Disturbed. Like the eng in the galor, it's a great ship. there's another final but can't remember the name of the ship >.< 13 alts...can't keep track sometimes.
shuttles...just kinda obvious why they're named that way i reckon.
U.S.S. Pinebox, fed freebie shuttle for vault mission
I.K.S. Coffin, kdf freebie shuttle for vault mission
Exploration Cruiser Retrofit (my current ride) : USS Yamato, in honor of the Enterprise D sister ship and the TNG Anniversery since i just got her a few days ago.
Tactical Escort Retrofit: USS Tiberium, based upon the Star Wars Lambda shuttle in SW Ep. VI. Flying causal takes a whole new meanining lol
Long Range Science Vessel Retrofit: USS Vyper, kind of wanted a name that stood for beautiful but deadly about her since Voyager always had the "run and hide" reputation about her but she still had teeth and never once did they "dumb the Borg" in the show.
Star Cruiser (our universe): USS Galactica, as a kid before Star Trek came into my life i always had a fondness over BSG the Original on TV.
Ive got more but those are the ones that i use the most or currently
Shuttle: U.S.S. Highlander - Danube Runabout: Because why not?
(Lt.) U.S.S. PT-109 - Shi'Kar Variant (with Centaur pylons and Miranda engines/weapon pod): It's named after the ship John F. Kennedy served on during WWII. It's a semi-famous ship.
(Lt. Comm.) U.S.S. Veranus - Excalibur Class: I could not come up with anything unique and better.
(Comm.) U.S.S. Stalingrad - Akira Class: Named after the battle.
(Capt.) U.S.S. Whitestar - Defiant Class: Babylon 5, which is an awesome show. (#2 on my list of favorite sci-fi tv series. #1 is TNG)
(Current) U.S.S. John F. Kennedy - Gryphon variant (with Dervish Saucer): John F. Kennedy was an awesome president and a strong leader. I know in the US military, only carriers are named after presidents, but this was named before the Atrox and I do what I want.
(Current) U.S.S. Iris Arc - Mirror Assault Cruiser variant (Just a hash of stuff that looked good together): A flagship in my own sci-fi universe idea. That's all I can say.
KDF Toon (the more "important" ships):
(Capt.) I.K.S. 'Iwro' - Vor'cha Attack Cruiser: I believe that's Klingon for Blood Fist, which is a name for one of my micro-machine ships, another Vor'cha, which has a red streak across the front section.
(Current) I.K.S. Qulqa' - Vo'Quv Carrier: Translate and see what else I'm a fan of (...at least until the next installment later this year ). You may have to switch the words to figure it out.
I've only passingly themed my characters. Only ones I really pre-planned were my sci Klink, using FF4 names: the Scarmilogne, Cagnazzo, Barbariccia, and Rubicante levelling up, with Rubicante, Golbez and Zeromus for endgame.
And my Ferengi who pretty much just referenced Nova while levelling up: Rick Chappy, Ginger Powder, Wiggling Niblets and LITTLE BOY. Yes, lame.