Great thread.
The one singularly strongest moment for me might be the end of "I Just Wasn't Made for These Times" where it does the round of repeating the title lyrics, and on the third time through it adds a downward chromatic chord progression not featured anywhere else in the song. It feels melancholic, but a little bit triumphant too- you can wallow in it but feel that better things are coming:
https://www.youtube.com/watch?v=NR7_TbMIVnA#t=02m40sBut I'll add, after linking it above, that it doesn't sound as good in isolation. As I'm sure with most of the moments here, it's the build and anticipation that makes them so strong. Or, with intros, it's what they're setting you up for. Tension and release!