Geez, where to begin with great guitarists? There are many many greats and some of it comes down to personal tastes too. Here are a few of my favorites:
Flamenco: Ottmar Liebert, Carlos Montoya, Al DiMeola
Full shred: Steve Vai, Joe Satriani, Eric Johnson, Gary Hoey, Mark Bonilla, Thayall, John Petrucci, Robin Trower, Jimmy Page, Jimi Hendrix, Yngwie Malmsteen, Kevin May, Eddie Van Halen, Nuno Bettencourt, Randy Rhoads, Santana, Allan Holdsworth, Steve Morse, Richie Blackmore, Rik Emmet, Tommy Shaw, Ted Nugent, Neal Schon
Jazz: Skunk Baxter, Pat Metheny, Lee Ritenour, Larry Carlton, George Benson
Blues: Stevie Ray Vaugh, Jimmie Vaughn, Eric Clapton, BB King, Bo Didley, Johnny Lang, Kenny Wayne Sheppard, Jeff Healey
Tasty licks/fills, great on rythm: Michael Schenker, Tony Carey, Ian Bairnson, Johnny Colla, Richie Sambora, Slash
Session Players: Stef Burns, Dan Huff
This list is just off the top of my head. I know there are others that are amazing.