Derelict uses Cthulhu mythos names for Shivan ships, such as Nyarlathotep. They work rather fine IMO, and there's a whoel bunch of them in Wikipedia. Other fictional mythologies such as Middle-earth mythologies (GTD IlĂșvatar, )
For Terran ships, regions of Earth are always a safe bet. True, it's used in many scifi universes but it just makes sense and the ship names are believable that way, so I don't see any reason why it shouldn't or couldn't be used in FS2 universe too. Another good source for terran ship names is obviously current navy warship names of different nationalities. And several mythologies also offer quite a bit of interesting ways to include hidden references and stuff like that. Using names from Irish mythology, Norse, German, Gaul, Indo-European, Sanskrit, Kalevala, perhaps even North American or Australian aborigine mythologies could be plausible - and certainly Christian mythos also offers a whole bunch of name candidates, but using for example names of archangels for Elysium transports might not suite the context - then again, it could be a hidden reference to something from behalf of the campaign maker. But names such as GTD Daghda, Belenos or CĂșchulainn just beg to be used.
And there's also the method of picking random words of some rare or fictional language (such as Sindarin, Finnish, Quenya and whatever you can think of). If it sounds good it usually passes, but it might be best to at least try and check the meaning of the word, though. Naming a destroyer GTD Ohramallas or GTC Humala might sound almost plausible to an english speaker, but for those who know Finnish they might cause slight amused chuckles. From English words, tere are some obvious adjectives and nouns that pass well as ship names, too - such as Impedance,
Famous people's names are excellent for Terran craft too. Science cruisers seem to be using that naming scheme a lot, but I don't see why it couldn't be used in other ships as well. Perhaps famous artists, writers and composers could work best as civilian ships - passenger liners and such.
Using only one kind of naming scheme throughout a campaign might become a little boring, so I guess it's best to use all kinds of name inventing strategies. The more variety the better in my opinion.