I would have to agree with EvilGenius that Credence kicks ass, but my favorite Opeth song i feel is underrated is Face of Melinda. that song fuckin rules.
Dirge For November - there are so many Opeth fans who dislike this song because it's "not progressive enough" or "boring"... but it's definitely amazing and not a single bit worse than all the other tracks on BWP.
I would say The Apostle In Triumph and the title track of Blackwater Park...I am VERY surprised more people don't like that one as much as I do. In my opinion Blackwater Park is one of the heaviest things they have ever done and is one of my favorite Opeth songs of all time!