Yeah, they've already been mentioned.
But the Nameless One is just plain awesome. There is nothing cooler, or more badass than him.
Garret, Threepwood and whatever the guy in Outlaws is called takes a nice second place.
I'm sure there's someone I'm missing, but most games have just awful protagonists. James, from Return to Krondor is almost worthy of a mention, far more personality than any games released nowadays. The problem with most games that have a "developed" protagonist is that they're not predefined. Fallout, Bloodlines, etc. It's your own character, and not a real protgonist, they can't really be judged like this.
I really would like to name another character, but I can't, both because the game hasn't even begun development, and because I can't say the name, but damn, that girl is awesome.
