Yeah, The Final Cut is just pure, unadulterated emotion...fantastic. I also find this line from Your Possible Pasts poignant:
Do you remember me
How we used to be
Don't you think we should be
There's also If, which I think is Roger's most intensely personal song...not apologizing for or justifying (as The Wall does) his inner self, just exposing it for the world to ponder.
But Jugband Blues is, to me, the most heartwrenching song in the entire Pink Floyd canon. Syd lays bare his psyche, and you can feel his pain in every note. The last stanza sends chills down my spine every time I hear it...
Wish You Were Here is just stunning. It's one of those songs that everyone can relate to, and apply to their own lives. I remember after 9/11, when Fred Durst and Johnny Rzeznick did that cover of WYWH, during that televised special. It was extremely moving because a lot of people were still missing at that point. Everytime I hear that song, it strikes a nerve.