Sometimes, I just name mine by set, if I decide I like a beta team enough to keep 'em. What I mean by 'set' is say, they'd all correspond to one another in some fashion. Maybe War, Famine, Death, Pestilence, Revelation, and then a filler would be a set, say.
That's the overused way, I suppose. Most of the time, however, I name 'em after Rp characters, either mine or a good friend's. It just makes the pixels that much more special and fun to go through the game with.
It's interesting hearing about how ya'll name yours.. And I have to say, those of you that can come up with original names are a lot more creative than I, and I daresay a lot of others - it's extremely hard naming things, even Pokemon. Very nice job you all do!