Well, at first I used to give them whatever names crossed my mind. When I played Pokemon Crystal, I named most of my pokemon after TPMers. But my adopted and captured pokemon are the only ones I've been keeping for a long time, and the adopted ones are the only onesI've really been paying attention to (well, there's Skydancer on my captured team, but even he has done nothing but battle), so I'm listing the adopted ones here.
Pidgeot: no name yet, even though he was my first pokemon. I might write an arc tgive him a name or something, but he might end up with a name like Spark, the way things are going.
Ninetales: Hero.
Kingdra: Water Angel. I didn't name her, she already had that name when I got her.
Vaporeon: Tsunami.
Venusaur: Sylvan.
Dragonite: Lagi.
Charizard: Amber.
Venomoth: Ventura.
Espeon: Caledor.
Stantler: Iael.