I use kind of a rock music motif, but I don't always stick to it that well. Examples from my current lineup:
Tenacious the Emboar: From Tenacious D, since only "TenaciousD" would fit, and I didn't want the name to look cramped. His nature and characteristic of "Bold, likes to fight" made me think of him as being tenacious.
Hall the Throh: If I ever catch a Sawk, I plan on naming it "Oates".
Dolby the Reuniclus: Named after Thomas Dolby, the guy that did "Blinded Me With Science". Again, not necessarily rock.
Dio the Archeops: Both are awesome but extinct.
Sabbath the Zekrom: Black Sabbath, of course!
Shook Me the Whiscash: From the AC/DC song "Shook Me All Night Long," since Whiscash is known for causing earthquakes.
I plan on doing an anime theme for Black Version, including Excalibur the Snivy...