Heartwarming: Ghost In The Shell Stand Alone Complex
The episode where one of the Tachikomas helps a little girl find her lost dog. It didn't have to help her, but it did.
The last scene of the first episode of season two, when the Tachikomas return. The look on Batou's face really said it all.
Earlier in the episode, in order to convince the Prime Minister to allow Section 9 to solve a hostage crisis, Aramaki offers himself up as the fall guy in case any of the hostages die. This shows the kind of faith he has in his team - he bets his own freedom that they will succeed. Which, of course, they do. They're Section 9.
The episode Affection in season 2 may be the most touching bit of backstory ever conceived. Kind of makes you hope that the Boy and Motoko find each other.