I think the most over-looked guitarist are the one's who don't shred 3 solo's in one song, but who are the one's that dare to try different things with the guitar. My pick (with just this moments thought) would have to be Tom Morello of Audioslave (ex-RageAgainsttheMachine). This guy is a genius with his creativity and playing style. Yeah, he using mostly effects to get those sounds, but who doesn't. I once saw Petrucci and his effects rack was almost as big as his amp.

Not bashing on any others, their playing style, or what they choose to do creative on the guitar. I just think guys/gals like Tom Morello deserve a tip of the hat.