I typically play as a custom race, the Amazons, so all of my ship types tend to have names relating to females and/or Greek mythology (the exception seems to be constructors, which somehow wound up getting names bragging about how fast they were, in French -- no, I don't know why I did that, either). I also change the name of my leader each game to that of a different mythological Amazon, but that's another story.
The naming system is, I must admit, a bit of a mishmash by now, with goofy absurdist puns and allusions ("Ms. Ile Fighter," "My Little Centaur," "Raft of the Medusa") mixed in with goddesses ("Hera," "Artemis," and, perhaps my favorites, the Furies, Alecto, Megaera, and Tisiphone, which specialize in Guns, Beams, and Missiles, respectively) and animals ("Tigress," "Lioness," and "Falcon" -- already a female name, since male raptors are called "Tercels").
Actually, for all that I may have seemed dismissive of silly puns and allusions, some of my favorite names involve those, for my specialty ships: My advanced freighters include the "Long Haul Sally" and "Mother Trucker" classes, and my new asteroid miners include the smallish "Clementine" and the seriously armed and armored "Molly Maguire" classes. Oh, and let's not forget my advanced survey ship, Dora, the explorer.