Favorite guitar players not named......

Chris Whitley (R.I.P.), Greg Koch, Mateus Asato, Jake Kiszka

I know that the guitarists that are listed as "household" names always make many lists for the best guitarists of all time, but for me, (except for Beck) they barely register. 

The blues bores me, and all those household names are limited to minor blues pentatonic playing. 

Prog:

Robert Fripp

Steve Howe

Franco Mussida (from Italian prog band PFM)

Steve Hackett, 

Steve Hillage

Phil Miller

Mike Johnson (from US avant-prog band, Thinking Plague)

Jazz:

John McLaughlin

Allan Holdsworth

Mary Halvorson

Ralph Towner

Max Sunyer (fusion guitarist from Spain)

Corrado Rustici (Italian fusion player)

These are only partial lists. 

Joe Satriani.

best there was, best there is, best that ever will be.

Duane Allman

Robbie Robertson

Nick Drake

I'd also like to make special mention of Bob Weir of the Grateful Dead. While not a lead player he developed a unique style of rhythm guitar playing designed to support the lead work of Garcia. Weir claims he was inspired by listening to McCoy Tyner comp on piano behind John Coltrane.