The ending of the Zombie Slayer challenge path. The sense of weariness and victory is so palpable that it's almost hard to believe that this is the same game that runs on They Might Be Giants references and the occasional sophomoric Your Mom joke.
The Avatar paths have some touching interactions between Boris, Jarlsberg, and Sneaky Pete:
Before you fight Boris as Jarlsberg, he sighs and bemoans the fact that the two of them are opposed. Boris considers him a friend, and if anything, was jealous of Jarlsberg for not having to work on his body as much as Boris has to.
Jarlsberg's parting words to the player at the end of the Avatar of Jarlsberg path are actually kind of sweet... in a grumpy-arrogant-old-mage kind of way.
In the Avatar of Sneaky Pete path, Pete's final words to Jarlsberg upon defeating him are quite touching.
One of the possible areas unlocked by using an Angry Jung Man familiar's dropped psychoanalytic jar is the Crackpot Mystic's Psychoses where you can defeat embodiments of his repressed fear, doubt, regret and anger. You start off in a Mega Man-inspired stage select screen, where the Crackpot Mystic's face (shown in the center) looks scared with his eyes darting from side to side and clicking on him will give the message, "This...this isn't me. This isn't me. This isn't me." If you succeed in defeating all the embodiments of his repressed fear, doubt, regret and anger, however, his scared face will be replaced by a smiling one and clicking on it will give the message, "Maybe everything is going to be all right after all." Aww.
The aftermath of the Little Canadia sidequest added on June 6th, 2013. After helping Marty gather presents for a lumberjill that he's sweet on, clicking on his shack afterwards reveals it went better than expected. The lumberjill's also revealed to be fairly attractive, subverting your character's cynical expectations that there would be an ironic twist, "like she'd have a beard, or was literally a goat, or something".
Dancing with Lady Spookyraven and being given a round of applause from the other ghosts.