All Butthole Surfers covers are great. I'm pretty sure I mentioned it in some other thread but their cover of American Woman by The Guess Who is ace.
Also the Aihiyo (keiji Haino's cover band) version of Satisfaction destroys all others.
Also, The Edgar Broughton Band did a two in one cover version of Apache and Dropout Boogie called, appropriately enough, Apache Dropout (I think). That is ace and a mashup decades before mashups were popular...sort of.
Royal Trux did a cover of Theme From Mash which is ace and kick the Manics' efforts arse.
The Rubinoos cover of I Think We're Alone Now but I don't think I've heard the original (Tommy James and the Shondells I think) but I can't imagine it's better. The Tiffany version is decent as well. Loads of people have covered it but those are the only two I've heard.