I haven't got names for all the team members listed in my signature yet, but I do have a few:
Emboar: Augustus. No meaning other than it's the name of Amy Pond's dad (in Doctor Who) and I thought it sounded good.
Excadrill: Simon. PIERCE THE HEAVENS WITH YOUR EXCADRILL
Serperior: Excalibur, just because of who his first form looks like.
However, when I played the Japanese versions, I nicknamed all my team members:
Simisear: Iroh, for the character from Avatar. I didn't want a generic-sounding name like "Flame" or "Blaze" what with the character limit and all, then I thought of characters from fiction who control fire and... yeah.
Whimsicott: Eli, for Eli Whitney, inventor of the cotton gin.
Swanna: Odett, which is supposed to be Odette but the blasted Japanese character limit is one too short. Swan Lake reference there.
Archeops: Ace, since the Pokemon is supposed to be so good and it just sounded right.
Scrafty: Scott, because I wanted to name something for Scott Pilgrim and that was who I chose.
Hydreigon: Drach, from the German for "dragon" (character limit came into play again), since I named him after the English names were leaked and we knew about the German wordplay.
Throh: Leroy, no particular reason.
Krookodile: Kroze, yes, the guy who works on YGOTAS. KROOOOOOZE
Swoobat: Bruce, since I once used Wayne for a Crobat. I should not have to explain this.
Cofagrigus: Atem, thought of at the same time as Kroze so I decided to go with another Yu-Gi-Oh joke. If there were more letters I may well have called him Dan Green.
Scolipede: Vyre, which has no meaning, just sounded cool.
Klinklang: Gizmo, just a word which fit a bunch of gears.
So yeah, there you go, a little insight into my naming process.