I just pick names I like which, strangly, usually happen to be hebrew in origin. When it comes to Pokemon, I base it off their trainer's personalities. Like in the fic that I haven't continued in years even though I still think about it (aka, Guilty by Design), the main antagonist was rather rash and uncreative, so he named the main Hitmonchan character Champ. Rival trainers tend to give their Pokemon "tough" names like Cyclone and Athena. For Rebecca's Persian, Calpurnia, that name always seemed kind of pleasant and motherly to me. Rebecca cares deeply for Pokemon, so I thought a nice name that wasn't too gentle (it still battles, after all) would fit the Persian.
edit: an exception to the trainer personality/pokemon name in Guilty is the hiker Boscoe and his Hitmonchik (a female Hitmon, ooooh) named Aya and a Rapidash named Uni. Of course, it's a bit strange really that a hefty guy would own "pretty" Pokemon anyhow. I like to think of Aya as being purchased or adopted or something, so she came with her name. As for Uni, well... it's an uncreative name, so maybe Boscoe isn't that great at names either.