Tool - Rosetta Stoned (vocals are already distorted so they could pretty much get away with growling these)
Katatonia - Black Session (a bit Opeth-ish already, that metal riff and the lead over it is somewhat similar to the same kinda thing in Harlequin Forest after the first verse)
Led Zeppelin - No Quarter or The Rain Song (no quarter has already proven itself to be appropriate for heavier covers unlike some more upbeat zeppelin songs, and the rain song is obviously just a great acoustic ballad)
Testament - Return to Serenity or The Formation of Damnation (well everyone in Opeth seems to love the formation of damnation, and return to serenity is just a metal ballad, welcome home (sanitarium) would work too)
Agalloch - In the Shadow of our Pale Companion
And they have to do some sabbath some time..