I'm not as well schooled on the older cats, but my votes go to Morello, Vai, EVH, Gilmour, SRV, Dimebag, Clapton, and Hendrix. Don't laugh, but John Mayer can play some stuff that I can't touch. I know he catches a lot of flack for his pop-trend, but break me off a little "Neon" or "Belief" and then we'll talk.
There is no way to be defenitive in saying who is the best off all-time.
Guys like Pettrucci/Vai/Satch/Malmsteen will blow you away with their technical ability but their music is so emotionaly detatched that you get bored after a few songs.
You have to be innovative with enough technical ability to play with the best of them and enough thought into the music that you don't seem like a robot pounding out as many notes as you can.
Hendrix is probably the best as far as a total package is concerned, then again there can be fair arguments made for several guys.
Frank Marino
Ronnie Montrose
Steve Hackett (Genesis)
Ry Cooder (should be high on the list)
Peter Green
Richard Lloyd (Television)
Tom Verlaine (Television)
Marc Bolan (T. Rex)
Marc Ribot (long time with Tom Waits)
Marc Moreland (Wall of Voodoo)
Robert Quine
Doug Martsch
Bill Kirchen
Alex Chilton
Jimmy Bryant