It is indeed impossible to choose one _BEST_ Opeth song, since all the albums are actually pretty different in style. Anyway, within the albums, I'm capable of ranking some song(s) above others.
On Orchid it is simple (for me at least) - Apostle in Triumph is the absolute masterpiece, which alone puts that (otherwise slightly inferior album) to the level of the other Opeth volumes.
Morningrise is the hardest case, although it has only five songs to choose from. To Bid You Farewell is great, but as it is so different from the others, it really can't be compared to them. That leaves us four, of which IMHO Advent and Nectar rise above the epic Black Rose Immortal and gloomy Night and the Silent Water. Of those two, it really depends, but at this very moment I like Nectar more.
On My Arms, Your Hearse there's a lot of "almost perfect" songs like When, Demon of the Fall and The Amen Corner, but I think they all lack something. Only Karma rises above that fine line between great and _GREAT_ - thus, my choice for that album would be Karma. Credence is again so special that I didn't take it into consideration - sometimes it is the best song on earth, but sometimes not...
On Still Life it is a hard contest between Moonlapse Vertigo and Serenity Painted Death, which are both incredible. It seems I can't choose at this moment, for I haven't listened the album today...
And on Blackwater Park, I guess it must be Bleak, which I'm listening at this very moment. Or then The Funeral Portrait, but I'm not that far yet.
-Villain (np: Bleak, as I said already)