The Afghan Whigs version of TLC's Creep is great, any of the songs that the Whigs covered really, but creep stands out.
Twilight Singers version of Bjork's Hyperballad is as good if not a bit better than Bjork's (and I love Bjork)
Travis covering Baby one more time is funny but good
I am sure there are others but those come to mind quickly
I'd rather be hated for who I am, than loved for who I am not