Some good choices here. I can't not pick just three, I am sorry.
My faves go as following:
Jason Becker
Steve Vai (The man quite possibly, is the most talented guitar players ever)
Buckethead
Ron Thal (If you haven't heard him, I highly suggest checking him out)
Mattias IA Eklundh (If you haven't heard him, I highly suggest checking him out)
Stanley Jordan
Eddie Van Halen (For his inovations on the guitar)
Dave Celantano (CHECK HIM OUT!!!)
Michael Fath
Michael Angelo Batio
Yngwie Malmsteen (Some people said he is the most natuarlly talented guitar player out there, he is not.)
Danny Gatton (I can't believe nobody mentioned his name!!!)
Alex Skolnik
Greg Howe (He is up there with Vai for most raw talent)
Guitarplayers I do no like or I think are overated:
Kirk Hammet: The man sucks, plain and simple. Sour notes galore, hides behind a wah pedal, shitty tone and rehashed pentatonic licks.
Carlos Santana: If I here one more Santana song on the radio, I am going to snap. He is soooooooo sour!
Eric Clapton: If you want to hear a fine blues guitarist in action, he is not that fine blues guitarist. There are so many blues/rock guitarist that give clapton a run for his money. He is just a name, IMO
Tom Morello:
I really can't stand him, don't know why, just can't. He couldn't hang with big boys, check out: "Guitars in the round"
As far as his "scratching" goes. Listen to Buckethead heads early stuff. He was doing it long before Morello and much much better.
Randy Rhodes: When I first started playing I was a huge RR fan but as I have gotten older and progressed on the guitar I have come to the conclusion, he wasn't that great, techincally speaking. His guitar tone was wretched and he was constantly out of tune. I will give credit were credit is due, he did influence a major part of heavy metal. I do take into consideration the time when was doing this but compared to todays standerds he is fairly weak. Check out Malmsteens first album for Neo-Classical at its best.
Jimmy Page: I can't stand him.