I'm a big fan of the Adventures manga, so I name every protagonist I play as in a Pokemon game after the Adventures protagonist of that game's arc, with only one exception. So far I've had (as Name - Game):
Ruby - Sapphire/AS
Diamond - Pearl
Gold - SoulSilver
Black - White
Titus - White 2
Ecks - X
Titus is the only name that doesn't fit the naming procedure, because I named him after the Cthulhu Mythos protagonist Titus Crow. I plan on doing another White 2 run under the name D.Kurou, short for Daijuji Kurou, the protagonist of the VN Deus Machina Demonbane, which fits thematically--Kurou sounding like "kuro", the Japanese word for "black", and the whole name being a loose Japanese translation of Titus Crow.
Ecks, arguably, might not fit, as it's not really a name, but I couldn't name a character the letter X and feel good about it.