Well this is entirely a matter of tastes, but I'm more than willing to tell you what my favorite Opeth tracks are...
In Mist She Was Standing, Ghost of Perdition, Hope Leaves, To Rid the Disease, The Drapery Falls, Deliverance, Master's Apprentices, Demon of the Fall, Under the Weeping Moon, The Moor, Godhead's Lament & A Fair Judgement