Sh!t, zillions of them. For starters:
Mogwai
My Morning Jacket
Carissa's Wierd
Dntel (hell even with his work on The Postal Service he really goes relatively unnoticed)
Four Tet
Modest Mouse (Well, up until recently. They've become popular with their worst album though, and their earlier stuff still goes unnoticed)
Neutral Milk Hotel
Twilight Singers
Sunny Day Real Estate (with the popularity of whiny emo sh!t you would think they would be in everyone and their mother's cd player)
Built to Spill
and to top it off Nick Drake
Now these artist's are quite popular in their own little small (and sometimes not so small) markets, but with the exception of Modest Mouse (and only because they changed what it is that makes them Modest Mouse, no more desolate western soundscapes and musings of the makeup of the universe) most people have never and will never hear of them.