How about these guitarists? Guitar is played all over the world, for all types of music and the Rolling Stone list forgets that. If someone has already mentioned the same folks, I'm just working from a list I came up with earlier when someone dared me to name guitarists better than Clapton, who voice is what I love. I hate pigeon-holing since great guitarists can play many types of music, so here are the names:

Mike Sterns
John Scofield
Peter Frampton
Pat Metheny
Glen Campbell
Wes Montgomery
Habib Koite
Franco
Ray Kane
Andre Segovia
Sonny Chillingsworth
Victor Wooten (he may play bass, but he's so fluid that it might as well be lead guitar)
Jaco Pastorius (same comment as for Victor)
Adrian Belew
George Benson
Larry Carlton
Hiram Bullock
Robben Ford
Stanley Jordan
Otis Rush
Ellmore James
Ellen McIllwain (Blues and she's amazing)
Bonnie Raitt
John Mayer (ignore the MTV rotation stuff)
Coco Montoya
Paul Brady
Pierre Ben Susan
Tommy Malone (Subdudes)
Manus Lunny
Andy Irvine
Garnett Rodgers
Leo Kottke
Chet Atkins
Vince Gill
Prince (he showed everyone why he was inducted into the Hall of Fame when he performed there) Neil Schon
Mick Taylor(the ignored Rolling Stone)