I've been naming my ships after famous boxers. Leonard, Robinson, Marciano, Clay, De La Hoya, Fraizer. It seems appropriate to me as I usually fly escorts, in essence the fighters ship class, and as a personal nod towards my grandfather who was a boxer himself.
My science ships were named first after Greek Cities, then Greek Landmarks (the Parthenon), and then finally I settled on great Philosophers and Scientists (Socrates, Aristotle, Plato, Archimedes)
My first Klingon was a mixed bag of names, after songs, using the name randomizer, and now I'm flying the I.K.S. Masamune
My second Fed had his cruisers named after Roman Emperors during the Pax Romana (Roman Peace), while my second Klingon had his cruisers named after Klingon Chancellors (save for my K'tinga who was named the I.K.S. Lord Kruge).
All my ships sport my favorite comic hero names. Across both factions. And each ship is colored to match their costumes. So if you see USS Wolverine flying around. Or my BOFF team with two green characters and a ****ed off canadian, it's me.
I generally run with a theme name for each character.
My KDF Tac used "adjective bird" for all ship names, this was back in the day when I got every ship at every level because it was done with EC and as a Klingon you where rolling in it. Shuttles are included in this them.
My Fed used two ship names for every ship he flew. All Cruisers had the same name. All Escorts as well, same registry number and I advanced the letter on it.
My Fed Science is using all random names that begin with A. Sometimes that is a lot of clicking.
My KDF Science isn't really being played so I haven't thought up a theme yet.
My Fed Tac will be using names from the game Space Pirate Amazon Ninja Catgirl, for ships and crew. Things like Bloodfur and Purrs in Shadow. And yes the game is referred to by an Acronym.
I have many ways to name my ships. Some have names from different series, Trek or non-trek. Some have something to do with certain tv-series episode names. One has the name of a star. The rest are whatever came to mind at that point.
But seriously, I'm happy to see you're giving it some thought. Too many playing this game name their ships after whatever they happened to have pulled out of their arse that morning. I ran across a ship named Poontang the other day. Poontang? Seriously? Here's a guy, thought I, who's just really not into the spirit of this whole Star Trek thing.
I look to the British Royal Navy. I like the way they name some of their ships with adjectives and nouns which are off the beaten path, i.e...
I tend to merge my two greatest obsessions, Star trek, and Tolkien!
All my Fed ships are names after places in Middle Earth (but the more obscure ones, NOT U.S.S. Shire/Gondor etc, Rather, Eriador, Belfalas, Arnor, Angmar) except My main ship, The Dreadnought, U.S.S. Annatar (Saurons "Good guy" handle, means Bringer of Gifts, called it that as I've ended up being too generous on this game [Kitted a stranger out with AP beams from mem alpha after 20mins of chatting! lol].)
As for my KDF Ships, all named with the random button as far as I know, (Rarely play him, always feel like I'm a traitor when I do! lol!) But HIS name is Melkor (Saurons Lord and Banished Leader for those who don't know!)