Todd telling Jenny that he would love her even if she was horribly obese. Keep in mind that Todd is horribly afraid of fat people.
The scene where Curtis tells Hannah he became the basketball team's mascot because his grandmother was a fan and this was the closest he could get to actually being on the team. Even if she turned out to be a Satanist, that was sweet.
Freak Love was a genuinely heartfelt musical number. It is quite possibly the main reason for the Curtis/Charlotte fanbase's strong existence.
Jimmy saving Todd from having his salami sliced by an invisible pervert.
Curtis' non-disastrous birthday party in Season 2. Also features a Big Damn Kiss between Curtis and Hannah.
The Todd/Jenny moments during Black Tie Showdown.
The end musical number in "2 Girls, 1 Tounge" features the gang apologizing for various things. Jenny's involves her staring out the window at Todd and his new girlfriend and singing "I'm so sorry I missed my chance." Before this episode, you wouldn't really have thought that Jenny returns Todd's feelings, but apparently she does.