The various comical ways Shinra's CommSpheres go down in Chapter 5, from being eaten by a dog to being pecked by a Chocobo to being punched out by Barthello.
This troper felt the scene where Beclem kicks a blitzball at Keepa was funny. When hit by the blitzball, Keepa flies backwards into a nearby wall. Also overlaps with awesome. Here's the vid http://www.youtube.com/watch?v=8z5bWWuyTSY
One of the funniest moments in the game for me was when Yuna saw a recording of "Tidus"trying so save someone named "Lenne". To say she did not take it well is an understatement. And it was hilarious.
Two, both related to Yuna's heroic tendencies. First there's the part where Yuna just can't say no to helping out, and Shinra's response is: "Hero. Summoner. Doormat." Then there's the part where Tobli is about to get Yuna to agree to sell tickets for him, and Paine figures out before she does that she's about to be roped into something she'll regret.