Normally I find it really hard to narrow favorites down to one, but in this case, it is easy.
Roine Stolt (The Flower Kings, Transatlantic)
I have not yet heard a guitarist who is better at injecting such raw emotion into his guitar playing. He's the very best elements of Jimi Hendrix, Carlos Santana, and David Gilmour. IMO (and I'll stress the "IMO" because I know pretty much everyone else on this board will disagree), for the most part shredding is crap. I used to, but no longer, give a rat's ass about how technical someone is. It's all about how much soul there is in it for me now. There are, though, a few who do shred that I really like, such as Petrucci (I like him for his slower solos with his great bluesy touch), and Michael Romeo (for his compositional brilliance).
EDIT: I don't mean to imply that MJR has no soul in his playing, though. While it is true that he often doesn't show it much, he does a great job in Accolade 2, Communion and the Oracle, DWoT, and Lady of the Snow.