I think my #1 most emotional Opeth moment has to be in BRI when he sings 'And your voice is vast and achromatic.... but still so precious'... when he whispers that last line it almost always brings me to tears/gives me chills.
#2 Would be the end of When.... I think most people know what I'm talking about.
Another would be the 'no one would know... ohhh oooohh' from Godhead's lament.
One I can't miss is definately the verse from my signature.
One song part that totally freaks me out every time I listen to it has to be the 'ahhh ahhh ahhh' part of White Cluster where Mikael sings along to the music... it just hits such a crescendo... I can totally imagine myself going crazy moshing when they play that live...
And also the 18 second growl section near the end of BRI... whenever I just hear those guitars come out of nowhere and Mikael's voice tearing shit up, it gives me chills.
The end of Dirge for November... I was hooked on that when I first got into BWP.
I also really like the hollow atmosphere of the start of Eternal Soul Torture... then \m/ when it goes into the distorted riff.
3:48 into In Mist She Was Standing, when that little acoustic interlude comes in... I learned to play that almost instantly after hearing it.
There are so many more that don't come to mind right now... but ALL OPETH MOMENTS ARE GREAT!!!