What I have enjoyed about reading this thread from start to finish is seeing some familiar faces that I like, listening to some great guitarists that I didn't know play at their peak, and seeing how others perceive "your" favorite guitarist.
While I wouldn't call these guys the best overall, I feel they were the best in their genre and used to and still listen to them alot:
Warren DeMartini (RATT)
Jerry Cantrell (Alice in Chains)
Nuno Bettencourt (Extreme)(III sides to Every Story is a great album)
And the list could go on.