Just off the top of my head:
He-Man 1980s: "The Problem With Power." A surprisingly emotional episode, even with the number of jumps the producers had to jump through to get it to air. (As in, He-Man was originally going to kill someone by accident. An innocent person, at that.) Even in its released form, it's by far the best episode of an otherwise "meh" to "please make it end" cartoon.
Hi Hi Puffy AmiYumi: Actually a couple from the last season. "The Golden Fleas" was two parts, allowing gags to develop and breathe for once. "Sitcomi Yumi" was a pretty decent mix of good references and a hilarious ending. "Sound Off" had some decent fourth wall jokes, including the single funniest gag in the series. (The entire production team falls asleep at their desks, including one guy just sprawled across the floor.) "It's Alive!" actually made good use of Frankenstein, and utilized the show's most annoying character well. Granted, the series itself was a massive pile of suck for the most part, but there were still a few microscopic beams of light mixed in.
Incredible Hulk, Marvel Super Heroes Version: The three episodes with the Leader using the Hulk to steal a device from the Watcher. (At seven minutes each, it technically added up to one episode.) Even with the...very limited animation the series was known for, the episode was a blast to watch. The voice acting was good for once, the fight scene was actually exciting rather than tedious, and the ending was downright perfect. (This was made even better when I found the comic issue it was based on...and found it to be a very faithful adaptation.)
That's all I can think of at the moment.