I agree with your mention of Squall actually. Even though he has all these obnoxious and imcompetent teammates (come on irvine you can't pull a trigger at crunch time?) and the revelations that come along during the game he still manages to keep cool for the most part and generally is quite the badass(that sword has got to weigh a ton!). Which is why FF8 is my second favorite final fantasy.
I pick Chrono from Chrono Trigger because he doesn't speak, has an awesome character design and he uses katanas. He did an awesome thing towards the end of the game (not going to say since it's spoilers).
Gary from pokemon would always be upbeat and cocky, even after you beat him five times in a row, he'd still have a witty one-liner to say before running off! I also kind of felt bad because his grandfather forgot his name, that was a weird plot device...
Quina from FFIX. There are great heros like Chrono or Cloud, terrible villains like Kefka of Ganon and beatiful girls like Zelda, but the coolest character ever is Quina. He/she/it is so random and funny and does not care about what others think of he/she/it.
He he, I love Ryu from Ninja Gaiden too. Well, he's a freakin' Ninja and he acts so Cool. Also, a hell of a game, I played it like a mad-man, really enjoyed it!