Sections that I've been told are too short:
1) "Am I like them" from "The Night and the Silent Water."
2) "Devious movements in your eyes" from "Bleak."
3) The instrumental, Castlevania-esque section near the middle-end of "Baying Hounds".
4) "Your memory's nothing but the scars on me" from "Deliverance."
5) "Making my way through... something... oh-oh-OH" part from "Godhead's Lament" (sorry, can't remember the exact lyrics at the moment, SL isn't one of my favorite Opeth albums).
And many others.
In fact, one of my friends told me that Opeth should've made ENTIRE SONGS from these sections alone.
I don't agree, but then, I don't really agree with you, either. I'm in the middle.