I'm not sure whether this song really gets the shaft or not when people talk about Queen's "A Night at the Opera", but "The Prophet's Song" was the first thing I had to think about when I saw the thread. It's an amazing piece IMHO which can take a while to get used to but which is terrific once you're into it. I've never seen it mentioned specifically.
I also had to think of another piece of Queen music although the album itself isn't that highly regarded, I guess. The very last track, "It's a Beautiful Day - Reprise", segues into IMHO a fascinating, very unusual and very beautiful piece of instrumental music (about a quarter of an hour long, if I'm not mistaken). It's a hidden track which completely took me by surprise, and I've never really seen it mentioned in reviews or other places.