My favourite guitarists would probably be:
(no particular order)

-Thurston Moore (Sonic Youth)
-Lee Ranaldo (Sonic Youth)
-Mauro Pawlowski (dEUS)
-Jimi Hendrix
-Captain Beefheart
-Johnny Marr (The Smiths)
-George Harrison (The Beatles)
-Josh Homme (Queens of the Stone Age)
-Frank Black (Pixies)
-Beck (NOT Jeff Beck!)
-Keith Richards (Rolling Stones)
-Pete Townshend (The Who)
-Rodrigo (from Rodrigo y Gabriela)
-John Frusciante (although I feel like the Red Hot Chili Peppers' songs didn't do justice to his talent, whe he was in that band)
-Tim Vanhamel (Millionaire)
-Jamie Hince (The Kills)

And of course Ron Asheton (The Stooges)

I know I'm still forgetting some, but these come to mind now.