Lately I've been naming the main character after people from my RPG Maker 2003 game. (Eiutah)
Most of the time I will make up names on the spot and use them for my games later down the road (Zacht, Staven, Tiana, Tjara, etc...)
Of course there's the obvious ones...
Cloud=Spikey/Chocobutt/Zack
Barret= Mistah T
RedXIII= Nanaki
Vivi= Puck ("Puck, huh? Kinda funny name... anyway my name's Puck!")
Steiner= Rusty (R-R-RUSTY!? MY NAME IS SIR ADELBERT RUSTY!)
Garnet=Garnet (Hmmm secret identity.... ooh! I know! I'll use my REAL name!)