The whole 23 minutes of Supper's Ready. After this colossal masterpiece, there is really no appropriate follow-up.
Totally agree with Stadler on Under Pressure. Truly a magic crescendo.
In The Air Tonight. I think I don't need to mention the exact part.
The finale of Relayer. While Gates Of Delirium is still the masterpiece of the album (and one of my top 3 songs of all time), the finale of To Be Over is one of the greatest and most touching parts ever for me. It might sound cheesy, but I always hear church bells in the background at the end, although I know that there are no church bells in this song. Anyone feel the same?
The "the rhythm has my soooooouuuuuul" part in the original recording of Peter Gabriel's The Rhythm Of The Heat.
And here's my guilty pleasure song: I absolutely adore Gotye's Somebody That I Used To Know. I never listen to it only once. For a prog fan, this song is just so damn short!
Also, I always sing (or better: scream) along with Kimbra when she (brilliantly) introduces the second chorus with " I wouldn't catch you hung up on somebody that you USED TO KNOOOOHOOOOOW".
Oh I just thought of another one: Marillion's Throw Me Out is also way too short (yet perfect just because of that) and I always listen to it at least twice. This is a song that seemingly no one cares for, but I just love it.