Awful Fantasy was the best ever.

Then in FFVII there were a few funny parts. The parts with Don Corneo were the funniest, especially if you're able to get Cloud in with him, and you play along, then Tifa and Aeris come and they're like, "Cloud, what are you doing?!"
lol
Then the funniest part in FFIX was when you first see Kuja, because he's wearing lingerie.