I think the band Fugazi is, essentially, the ultimate indie band. They have remained off of major labels and truly independent in their way of doing things - yet sell pretty well.
Of course, they also make super music.
Check out The Argument, Fugazi's latest offering......it's......"post-punk"......but......wow......
I also think that the indie band Dredg doesn't get enough attention.
And basically, Radiohead gets way too much attention - and way too little.
They aren't really revolutionizing rock and roll, IMO, but they do some really interesting things, musically, that I don't feel get enough recognition.
Nine Inch Nails may be the most under-rated band of all time, though NIN worshippers (read as: one of my best friends) can be damn annoying.
Tool is definetely over-rated.......but they have the same thing as Radiohead - their musical ideas don't get enough recognition......(Pyramid Song & The Grudge by those two bands both have this weird pseudo-swing thing going on.......).
Asian Underground stuff is super, and not very popular.
And of course, American Folk music is a super genre that is often over-looked...