I don't claim to know them all, but these are a few of my favorites.

Jeff Beck--All around great guitar player, occasionally I wish he'd sound less unique but generally I love his playing. He straddles the line between the blues of the late 60's and the shredding of the 70's & 80's and continues to play at the top of his game.

Steve Vai doesn't have the greatest tone to me but has the Beck quality of playing music, and not just showing off, and at the same time showing off HIs musicality separates him from other shredders, except maybe Satriani, but I feel Vai is more complete, and that is what this style is about--total mastery.

Robben Ford--sort of a subset of Larry Carlton, perhaps, but I simply prefer his playing. Smooth jazzy blues, always with some mystery notes that elevate the song in a natural sounding way. Incredible tone & feel, perhaps lacking all out aggression or abandon.

John Frusciante--doesn't really do anything new, but he fills out the Chili Peppers, and takes something that might sound a little empty and makes it lush with melody, passion, beautiful tone. I like that he is not trying to stand out but absolutely serving the music. That's the collective spirit of the RHCP in my opinion.

honorable mention:

I also love George Benson's playing, Eddie Van Valen for what he contributed to guitar (and still plays amazingly, if from a bag of tricks) and The Edge, not for his technique, exactly, but for how he shapes the sound of his band and his obvious style
[Edited 5/25/10 13:21pm]

Joe Satriani gets no love?

Jimmy Page

No mention of RICHIE KOTZEN so far???

Great tone, excellent technique and one hell of a voice...

My three best are:

Eric Gales, Gary Moore, Jeff Beck

I have to give mention to the following that were not named by anyone:

Andy Timmons
Gary Hoey
Kenny Wayne Sheppard
Tony MacAlpine
Vinnie Moore
Andy Aledort
Robert Cray
Paul Gilbert

And in defense of Ernie Isley, who I think is an excellent guitarist, everyone has mentioned the music with the Isley Bros, which I think his playing showed range (even though trapped inside of R&B), but his solo cd, High Wire, showed his guitar ability and his musical ability, since he did all the instuments and vocals on the cd.

Best is an apples.oranges thing but I listen 2 these cat's music pretty often....

David Hildago (Los Lobos)

David Whild (Outkast, Whild Peach

O'Dell (Mint Condition)

Jesse Johnson

Norman Brown

Robert Randolph

Dave Matthews

Holy shit... how come I've never been hipped to Frank Gambale before? I musta been sleepin' to miss this guy but I just stumbled across him on youtube.

Incredibly fast player and he makes it look effortless.

[Edited 7/9/10 1:02am]

Prince

Jesse Johnson

Robbie Krieger (The Doors)