Daniel Ash from Love & Rockets and Bauhaus. He has a very unique style bouncing between complex picking and machine-gun tempo strumming. He is able to play live with Rush-like sound complexity and impeccable timing.
Juliana Hatfield has very creative structure and modified chord phrasings. She is a very underrated contributor to 90s grunge/alternative guitar style.
The guy (I can’t remember his name) from the FIXX.
Johnny Marr, I don’t know if he is tehnically a great guitar player, but he is a fabulous songwriter who uses his guitear to fantastic effect.
Danny Gatton
Yeah - we’re splitting hairs. Trucks is less well-known but VERY highly-regarded by those who know of him (including, now, **Endiqua **- very cool! and you should check out his prior CD, Songlines, too - track 3 is worth the price of admission alone but it all rocks, 'cept for Crow Jane ;)). Pete and Keef are super-well-known but typically not counted in the Pantheon of gunslingers…
**THespos **- yeah, I hear you about stuff you used to dig. Most of it doesn’t hold up at all, which is sometimes tough to admit. But some stuff does! If you haven’t listened to UFO’s live album, Strangers in the Night, lately, give it a whirl. Lights Out, Rock Bottom, Too Hot to Handle, with Michael Schenker on lead - it’s all good!
I looked up the Moore C-90P - looks like a totally hot shredder; makes sense side-by-side with an EBMM VH model (and yeah, some of those are getting totally collectible). But I gotta say - I don’t speak shred on guitar. I would look like a total moron trying to at least play Crazy Train or something…
I’m going to nominate Nils Lofgren. He’s obviously famous because he has been in Springsteen’s band for over 20 years, but because of the nature of that band, he doesn’t get to show his skills to their full extent very often.
I think that his work with his band Grin has been largely forgotten. His solo albums in the 70s after Grin broke up sold pretty well, but his albums since then have not sold well. I’m a fan, but I really think Nils is too weak a singer and song writer to be any more successful than he is as a solo artist. He needs to be in a band with another singer and song writer, and of course he is in one, but it’s not the kind of band that allows him to shine.
I think that he is a highly-skilled and interesting electric guitarist. He plays with a thumb-pick and incorporates touch harmonics, hybrid picking, and volume knob effects into his solos and fills very effectively. His solos are usually composed, I think, and are quite melodic. He is one of my favorite guitarists to listen to. A lot of guitarists I know are aware of him only as one of Springsteen’s guitarists. As Bruce said of him during his Hall of Fame induction speech, he’s the most over-qualified second guitar player in the world.
Jamie West-Oram in the Fixx. King of the 80’s clean/chorused sound. In the same camp, but IMHO much better, was **Gary Sanford **in Joe Jackson’s band - excellent job playing little chordy bursts of sound up the neck - anything from Sunday Papers and Different for Girls to the harder stuff of Throw it Away and Got the time…
Johnny Marr is a great, great player - again, not that underrated. He’s one of those guys who folks hold out as an anti-guitar hero, like Andy Summers of the Police and The Edge…but still a form of hero…
It seems like that’s the crux of the discussion about several of the names that have shown up on this list (like Trucks and Brian May)…they’re guitarists who are very well-regarded among serious fans of their genre (and serious fans of guitar playing in general), but are not particularly visible to the more casual music fan.
I’ve seen the late, great Danny Gatton’s name a couple of times in this thread. I don’t want to pick a fight with anyone :), but while Gatton is not very famous, I wouldn’t consider him under-rated. Among those who know who he is, he is pretty universally regarded as having been a great player.
On preview, I see that several others have brought up the under-known versus under-rated question.
You’re right - and I would say the same thing about your nomination, Nils Lofgren. Amongst players, he is highly respected - heck, he used to be able to do a back flip on stage while playing; that’s gotta count for something! 
And that’s why I try to differentiate between my should-be-more-famous guys like Beck and Setzer vs. my may-be-famous-but-not-held-out-as-a-great-guitarist folks like Richards, Townshend, Ramone and Young…doesn’t mean I got it right, only that I was trying to differentiate!
Seconding (thirding, whatever) Johnny Marr, Mick Jones and Prince. What’s Peter Buck’s standing among guitar players? He seems to be pretty underrated to me, but maybe he gets more credit than I realize.
Also from my 80s punk youth, Bob Mould (Husker Du, Sugar) seems to me to have been far more influential than his name recognition would indicate. Similarly, the late, great Bob Stinson of the Replacements, whose work was overshadowed by his shenanigans, was actually a pretty great lead player. And Curt Kirkwood of The Meat Puppets.
Finally, though he’s been solo for years, Robyn Hitchcock started out in the Soft Boys and had a real band (The Egyptians) backing him for quite a while, so he technically falls into the “group” thing, and is almost universally ignored for his playing skill (as opposed to songwriting).
Here’s some that aren’t mentioned that often in such lists:
Colin James
Billy Gibbons of ZZ Top
Steve Gaines and [b’Ed King** of Lynyrd Skynyrd.
Nels Cline of Wilco
But ** Derek Trucks** has been declared a new guitar god 
along with John Frusciante (mentioned above) and John Mayer (curiously not mentioned - possibly it’s still fashionable to dis him) on the cover of Rolling Stone. He also seems to grace the covers of guitar magazines with some regularity. So while he still seems to glide below the radar of the general public he gets accolades galore from that section of the crowd that values the art of the instrument.
I think that a lot of the discussion in this thread is stumbling on the term underrated by assuming it means “less popular”.
Kinda like I had first thought of submitting JoeBonamassa as underrated but he gets a lot of recognition in guitar enthusiast circles. So I don’t consider him to be underrated. Many albums and performances later he’s still unknown to the general public.
My thoughts about Richard Thompson. The public have no clue who he is. Guitar players, OTOH…
The late Terry Kath of Chicago deserves a mention here. We’re not talking the ballad with strings mushy schmalzy Chicago of the late 70s and 80s. We’re talking the genesis of the group.
According to Kath’s MTV biography:
The dude could play. He could sing. He could scream! Listen to his chops on the iconic 25 or 6 to 4 or the lesser known Free Form Guitar off the first album.
Agreed on Terry Kath. Love his playing on 25 or 6 to 4. That comes up on my iPod all the time and I’ll listen every time.
Joe Bonamassa is reasonably good, but is starting to fall victim to whatever disease causes Steve Vai and Joe Satriani to play without soul. I loved Bonamassa’s playing on the Bloodline record, and went to go see the group at a bar on Long Island as a result. He blew me away back then. However, I bought “You and Me” recently and immediately wanted a refund.
I’ll also second the mention of Billy Gibbons. I think he’s well-known in guitarist circles, but I don’t think the general population is aware of how influential he is.
Peter Buck is respected for, as his bassist Mike Mills likes to say - “the best right hand in the business” (don’t know if I’d want my bass player talkin’ 'bout me like that! ;)) Basically he can do jangly flatpicking better than most out there - and is highly regarded for it.
Joe Bonamassa, Richard Thompson, certainly Danny “The Humbler” Gatton and even Nels Cline are all inside-baseball guitarist’s guitarists…
John Mayer is actually pretty well respected, but there is always the inevitable working through his celebrity and schmaltzy ballad work, but his skill as a player is typically acknowledged. It doesn’t hurt that he has a Signature Strat that has become popular for the various features it combines.
ETA: Terry Kath - no argument, but he is more of a story than anything. “Yeah, he was great but came to a tragic end way too young” - he was a great player and singer and I keep his stuff on when it pops on, but I don’t know that he would’ve jumped to the top of the Gunslinger list if he continued to play - he’s in a band competing for time and mix space with a horn section, which electric guitars are typically set up to replace in small-combo rock bands…
Alex Lifeson is obvious!!
Not so obvious:
John Petrucci from Dream Theater. Amazing guitarist, held his own with Satriani on the G3 tour.
Joey Eppard from the band Three. Look up his stuff on Youtube, he’s amazing.
I would have included Thompson but for the band restriction - Fairport Convention was eons ago…
I don’t really know anything about Lita Ford, but “Crazy On You” is a Heart song and that would be Nancy Wilson playing the guitar at the beginning.
When Rolling Stone did a list of the greatest guitarists once, they placed Pete Townshend at number 50.
That officially makes him the most underrated.