Alrighty, I'll run through a few.
Audioslave: When they were around, they had a super line-up, though unfortunately, their latest and most critically tarnished album "Revelations" failed to sell even 300,000 copies if I recall correctly. In my opinion it was a decent album, though nothing compared to the groundbreaking self titled debut album. In general I think Chris Cornell is rather underrated, he's a fantastic singer. Do remember that he sung for Soundgarden and pushed onto Audioslave who also contained members of Rage Against the Machine. They disbanded due to silly disputes between the members, including Tom Morello who felt their music was too simple and that he wasn't getting enough time in the lime light. Though in my opinion he's slightly overrated as a guitarist. He hasn't written too many great pieces. Anyway, Audioslave have a nice back catalogue and weren't huge after their release of Out of Exile which is also another fantastic album. Unfortunately, they never got enough critical acclaim to fill their egos. They went down in flames like so many other "super bands"
Alice in Chains: Mainly because they're wuite unrecognised as the great Grunge band they should have been. Ten is a great album and one of the greats of the time in my opinion. I think they get a lot of beef thrown their way due to the front man also taking his own life, people see that as just another Rock n' Roll stunt and is the reason for their sucess. I can see it for Nirvana, but not for Alice in Chains. Not a majorly underrated band due to their lack of albums but worth mentioning no doubt,
Biffy Clyro: The band that hail form Scotland 5 albums. They weren't recognised until Puzzles which was their 4th and before then were reletively unknown. Their mainstream sucess didn't come until 11 years after they formed, and dwindled down again after the release of in my opinion, their best album "Only Revolutions". Though not very underrated I cant imagine that they're very popular outside of the UK and Ireland, thus leading me to say that they're rather underrated. They have experianced a lot of sucess yet it doesn't seem like they're as influential as they should be.
Bloodhound Gang: Now the first thing you'll think of is "Bad Touch" and you'll say well they're just one hit wonders. Well, they've got a lot of great stuff. "Hooray for Boobies" is fantastic, it's thick with random lines that just manage to stick in your mind. Jimmy Pop writes extremely clever lyrics and is unrecognised for them. Though Bloodhound Gang aren't what you'd call a strictly mature band, they do what they do and are more or less in their own league while doing it. Not many bands pull off what you may call "comedy rock" very well. In my opinion, they're far better than the likes of Tenatious D. They've sold (and this may be to your suprise) over 6 million albums, yet they're still rather underrated in the media. They've been critically acclaimed for songs like "Fire Water Burn" which is by no means their best or even one of them.
Creed: They were huge in America thanks to the songs "My Sacrifice" and "With Arms Wide Open" but outside of the US they don't seem to be as well recognised. They're extremely talented musicans and thier frontman has one fantastic voice. It's hard not to like it. The ironic thing about them is, they'd be considered heavy rock yet another label strongly enforced upon them is Christian Rock. Creed disbanded a few years back yet it's evident that they haven't reached the sucess they could have.
Damien Rice: An easy listening singer/song writer with fantastic talent. Best known for his hit single "Cannonball" on the album intitled simply "0". I feel he's very underrated and should be put on a stage with the likes of David Gray, or at least, not far behind him. Assisted by Lisa Hannigan in his first two albums he's a very delightful and different artist. It's something you'd listen to for many reasons, it can inspire you, make you doze off or just relax you in general. The acoustic guitar work on his albums is next to fantastic.
The Doors: One of the best bands to surface this millenia yet they're shadowed with hatred and disgust by many and for what reason? perfectly great song writers and have a back catalogue of very entrancing ablums.
Dragonforce: Haha not.
In Flames: Very much respected in the world of melodic metal, but unfortunately that world doesn't hold much competition other than "At The Gates". In Flames hold 11 studio albums and have been going from just the early 90's. Br far one of the metal greats yet you don't ever hear much about them at all. Besides, they've also done a collaboration with Pendulum, how many metal bands can say that?
Jack Johnson: A great artist and a great voice. There's not a lot else you can say about him really but he really is a joy to listen to, I can't think of anyone I've known that hasn't taken a shine to his music. Very easy to listen to and he's a very talented acoustic guitarist. He just deserves that little bit more recognition.
Lou Reed: is also worth a mention. Transformer is a great album.
MGMT: Someone already mentioned them, but worth adding to that they're quite an enthusiastic and creative bunch of young artists. There are so many Indie bands out there and MGMT are that band that have added a little bit more innovation into their music compared to the others.
Nightwish: I bloody love their style. Different to Within Temptation they also have quite good male singers. Have a look at "Bye Bye Beautiful" as an example. Only thing is I wouldn't say she's as strong a singer as Christina Scabbia. The male singer is very powerful though and should sing more often. Though there is a great contrast between their voices. Scandinavian metal is certainly on the rise after Lordi.
Pantera: A very influential metal band yet they were always over shadowed by the likes of Metallica, also held one of the most respected guitarists Dimebag Darrel who was the instigator of the famous technique the "Divebomb". Unfortunately he was shot on stage and was never replaced. Pantera are very underrated and have held that injustice throughout their lifespan.
Shadows Fall: Another young metal band that are in deserving of recognition. Very powerful guitarists and in general, very good musicians. A good frontman also, which seems to be rare in metal these days. If you listen to "Another Hero Lost" you'll know exactly how well he can sing. Redemption is also recommended.
Within Temptaion: Also been mentioned but in my opinion are quite a bit better than Nightwish. Probably the kings or even, queen, of the scandinavian metal scene. Though, they're Dutch, when quite a lot of the metal bands seem to come from Finland.
Almost mentioned Muse but I don't think they're so much underrated now as they were say, a year or two ago. They've really blasted onto the scene.