Frank Zappa is an odd case. Certainly not underrated by music enthusiasts, but because his guitar work is so varied and peppered about his songs inbetween the ‘wierd’ and/or ‘funny’ stuff, it’s not readily accessible to non-fans. And that’s the way he probably wanted it.
I’m sorry but Gilmour and Iommi don’t really fit the pattern of what I was talking about in the OP. Gilmour and Iommi have been praised ad nauseum(deservedly so, don’t get me wrong). I’m looking for guitarists that if you mentioned their names to the average casual rock fan the average response would be “Who? Them? Really?!?!”
I will totally agree on Bob Mould and especially Jamie West-Oram. I was fortunate enough to see The Fixx live back in '83 and they were actually the opening act for A Flock of Seagulls. Needless to say, we enjoyed the opener a LOT more.
Chris W
I have to chime in with Rib Eye, Dave Murray and Adrian Smith of Iron Maiden are soooo good, and have soooo little credit thrown their way. Definitely the best pair of guitarists ever.
I do not put their buddy Janick Gers in the same boat as I think he is too sloppy, but definitely Dave and H!!!
Most rhythmn guitarists are vastly underrated for the job they do, IMO. You always hear about the main guy, but never about the guy in the background keeping him going…
I agree with whoever said Brian May. Nobody ever gives this guy his due respect.
Alex Lifeson of Rush.
Hey rsvp9146!
Have to disagree with Steve Howe being underrated. He’s the best in the world. You know it, I know it and so does the rest of the world! Maybe underappreciated, but not underrated! 
Somebodys gotta go back and get a shitload of dimes.
Mick Ronson
Just know of him from his work with Ian Hunter
Pat Smear (Germs/Nirvana/Foo Fighters)
I agree with Lifeson, who I’ve never heard mentioned unless I directly ask about the guy. I think Gilmour is pretty well respected… but this is all from a guitar player’s perspective. I have no idea what people who don’t play think, or even if its different from what I think!
Billy Corgan o the Smashing Pumpkins is a talented player. Think what you will, but I’ve heard him shred it up like a mmmaaannniiiaaccc. Who else… I don’t know, more to come as they are remembered
Don Felder
I always thought Steve Jones from the Sex Pistols was an under-rated guitarist. Not fancy, but under-rated.
Joe Walsh as a guitarist, IMHO
Kerry Livgren-Kansas
Dickie Betts-Allman Brothers
John Fogerty
Arlo Guthrie (yeah, he’s a folkie)
Patrick Simmons and Tom Johnston-Dubious Bros.
Denny Dias-Steeley Dan
Jeff “Skunk” Baxter-Steeley Dan / Doob’s
Larry Crane-John Mellencamp
I’ve debated posting this one, because he does get some respect, but no one seems to know about his solo stuff:
Jerry Cantrell.
Yes, I know that Alice in Chains was a fairly popular band, but he doesn’t seem to get any recognition. Go out and buy one of the Degradation Trip albums, either the one- or two-disc version, and see what a musical talent this guy is.
Waddy Wachtel
RIGHT ON!
Mick Ronson was Bowie’s guitarist for The Man Who Sold the World, and Ziggy as well. The Man is a totally ass kickin power trio extravaganza!
Peter Buck of R.E.M. comes to mind as being very underrated. He’s said in interviews that all his stuff is pretty much based on C, G, and D chords and simple arpeggio patterns, but I think it takes a lot of skill and creativity to keep that simple sound fresh over 20 years and a dozen albums.
I agree with Alex lifeson and I would also still defend Iommi as underrated simply because I don’t think he really gets the recognition he deserves for basically creating the template for heavy metal riffing.
Dave Gregory (XTC) and Jason Falkner.
Tom Petty’s right hand man, Mike Campbell, has never gotten the credit he deserves, IMHO.