The most underrated Opeth song: All Of Them
If they weren't underrated, you'd hear them much more on the radio and such. It's a pity that such talent gets stuck in a "cult following" scenario, while bands like Metallica, Megadeth, etc (all have decent musical ability) get huge accolades, much publicity, and fame and fortune (for whatever that's worth).
Confined to this board, I think almost all songs have been listed as someones favorite, but Karma and The Amen Corner get the least recognition. I'll also add The Leper Affinity to the list.