Dr. Naomi from No More Heroes/2

Probably Vincent from Final Fantasy VII. He's a character that you can play the game through, without even seeing him. He's not a must have character, he's totally optional and secret.

Yet... He had his own game in Dirge of Cerberus and gets a good portion of time in Advent Children. He appears in Before Crisis, he's unlockable in Ehrgeiz and Cloud in Kingdom Hearts was designed around the look of Vincent.

He's cool. He's well known.

i loved daxter's wit and humour in jak 2 and jak 3

I'm also partial to Shadow from Final Fantasy 6.

He's a purely optional character who almost seems like more trouble than he's worth, but he has a great side-story and is possibly the most fun (and well-designed) person in the game. His character just exudes coolness, and he also has the powerful dog in all of gaming.

I say melchior from Chrono Trigger is a BOSS!

Despite all the hate, I actually found Steve from Resident Evil: Code Veronica to be pretty cool, if not a little annoying. When he was captured and killed near the end, I actually felt pretty bad for him.

Another would be Cliff Fittir for Star Ocean: Till the end of time. Not the main character but a bit of major character. He's pretty boss and is a freaking monster in your team. You can Hammer of Might your way through any poor bastard dumb enough to get hit by it. Pretty much rapes anything with that one move for the first 50 lvs of the game. He was also a nice contrast to worrisome and whiny fayt.

Julia and Raine from Final Fantasy 8. Ellone as well, but I am not sure if she constitutes a minor character.

Hmmmm auron from FFX and more recently charlie cutter in uncharted 3, he is awesome!

Haha I forgot about that line