All of the following come up twice:
Solitude - Black Sabbath (Covered by Ulver)
Sabbath Bloody Sabbath - Black Sabbath (Covered by Amon Amarth)
Circle of the Tyrant - Celtic Frost (Covered by Opeth)
21st Century Schizoid Man - King Crimson (Covered by Shining)
Orgasmatron - Motorhead (Covered by Sepultura)
Gypsy - Mercyful Fate (Covered by Emperor)
Painkiller - Judas Priest (Covered by Death)
Leprosy - Death (Covered by Akercocke)
Sworn - Emperor (Remixed by Ulver)
And all the tracks on Nevermind that appear on Nirvana's self titled compilation, plus a shitload of live versions, demo's and tracks from EP's that made it onto albums which I can't be arsed to list. I don't think I have anything in my collection that comes up 3 times or more.
EDIT: Wait! Actually Kingdom Gone by At the Gates comes up 3 times; with the original and a bonus live version on The Red in the Sky is Ours and another live version on Terminal Spirit Disease.