I don't really dig the cartoon much anymore, so I don't have a favourite anymore. Trying to recall what I used to like.

The Golden lagoon was kinda cool, but everyone being gold just seemed like a cheap copout to save the cell painters painting all the TF's details, that bugged me even when I was a kid. The same with that damned Hate Plague when everyone turns red.

I think my favourite TF episode was the Ultimate Doom part one, if only because it had a really cool cliffhanger where Prime seemingly doomed earth (the best cliffhangers are those where it seems like the good guys are totally screwed like TNG's Best of Both Worlds part 1 and BSG's Pegasus) I hated waiting for the next ep back then, but a good edge of your seat cliffhanger is always memorable (even when they do a cheap fix next episode). Heavy Metal War also seems to resonate in my memory, however last time I watched it, it wasn't so special.