Personally, I think that any list that doesn't have Hendrix at the top of it is absolutely bogus...
I still remember seeing one of my dad's Neil Young albums, on which Neil is wearing a button that says "Hendrix is God".
Or Pete Townshend talking in amazement about a show where "The Who" and Hendrix got into an argument about who would play last. Hendrix ended up having to go first, and after he blew the crowd away, he walked off the stage and said "Follow that motherfuckers." Pete admitted that they couldn't.
Or Paul McCartney going to a Hendrix just a week after Sgt. Pepper's came out. Hendrix found out that the lads from Liverpool were there, and then proceeded to play the half the album in the middle of his first set.
The man was the most influential guitarist of all time, and able to do anything, and I mean anything on a guitar. Musicians bowed down to him. Clapton continually pays homage. Steve Vai wrote "Boy from Seattle" to emulate him. Stevie Ray loved him too.
Quick throw in--- Jimi's Favorite Guitarist - Billy Gibbons from ZZ Top
Anyway, I think it's unfair to even try and make a list without breaking it into decades. The technological advances made from decade to decade make it near impossible to compare different eras. What could Jimi have done witha processor? What could Eddie have done with just a tube amp?etc.
1950 and earleir: Joe Pass (Jazz), Les Paul (Blues, named the guitar after him didn't they?), Chuck Berry (Rock)
1960s: B.B. King (Blues), Jimi Hendrix (Rock brought the wah pedal to use), Paul Simon (Folk)
1970s: Jimmy Page - Led Zeppelin (Rock), Frank Zappa - (I guess you could call it Jazz)
1980s: Eddie van Halen - VH (invented tapping), and Slash -Guns and Roses
1990s: Tom Morello- Rage and Trey Anastasio - Phish
Others that haven't been mentioned in this thread...
Jerry Garcia, Grateful Dead - one of the best jam guitarists of all time.
Dave Matthews - some of the most inventive chords ever.
Nuno Bettencourt, Extreme - Flight of the Bumblebee anyone?