Whenever I try using a theme to name my pokemon, it just doesn't end up sounding right. So I just name them whatever comes to mind. I nicknamed my entire in-game team in White, except Registeel and Mienshao. Mienshao was received in a trade, so yeah.
My Serperior is named Smugleaf, for obvious reasons.
Archeops is named Broodonkus. I'm not really sure where that one came from, but it somehow sounds prehistoric.
Seismitoad is named Slippy, after the Star Fox character.
I haven't named Registeel, but if I could, it would be named Registall because he's so good at stalling.
Volcarona is named Enfuego, which I believe is Spanish for "on fire".
Sometimes, if I have a really good nickname on another game, I use the same nickname in another game. For example, I named a Remoraid "Diddely" in my Pearl and I thought it was the cutest nickname in the history of nicknames. However, that was a female one, so when I caught a male remoraid, I couldn't call it the same thing. So I named it Wendel. Now, if I catch a remoraid in any other game, I name it Diddely or Wendel, depending on whether it's male or female.