I can list song after song in this thread, but I'll limit it to a few or so for now.
personally I think Pain Of Salvation has countless 'beautiful' moments in their songs such as:
Pain Of Salvation - Foreword (the vocal harmonies when they sing "I'm not afraid anymore, including the entire interlude with the solos and the 2nd interlude or verse or whatever you call it).
Pain Of Salvation - Leaving Entropia 12:5 version (the piano parts)
Pain Of Salvation - Reconciliation (the high pitched singing towards the end)
Ok now for other bands:
Symphony X - Odyssey (the ending with the Choir when Russell is singing "this is the end of my odyssey")
Symphony X - The Edge Of Forever (intro piano)
Symphony X - The Divine Wings of Tragedy (the quick break and beyond, right after the massive soloing towards the end of the song).
Symphony X - Awakenings (the intro)
Symphony X - Accolade II (the first pre-chorus with the "aaah AAAAH" vocals)
Alright enough SX for now
Opeth, like PoS has a million of them, but here are a few:
Opeth - When (the first interlude right after the solo)
Opeth - The Amen Corner (the first acoustic interlude)
Opeth - To Bid You Farewell (the entire song, especially the ending)
there's so much more I might take up the entire thread, but I'll leave it here for now.