Of full songs (ie. not counting silhouette, prologue, etc.) I must say I like the least Dirge for November and April Ethereal. Also, I'm not too fond of Godhead's Lament and In Mist She Was Standing, although both those songs have some great moments. The Leper Affinity isn't very high on my list, either.
And I don't like some of the moments on Black Rose Immortal - it could be a perfect song, but it just isn't!
Nectar, on the other hand, is definitely among top-five Opeth-songs, IMHO. And I think Karma is the the second-best (after When) song from MAYH.
-Villain