That's another one, way funnier than the show's latest seasons for sure. :D

The first games I think of are the Ratchet & Clank games, I really like their comedy.
Kid Icarus Uprising and the Paper Mario games also had good hilarious moments.
The skits (little conversations between the characters) in Tales of Graces also made me laugh

Ratchet and Clank Series, Uncharted Series and The Simpsons Game.

The Stanley Parable, Grim Fandango, Portal 2. Broken Age had it's moments too.

Edit: Skyward Sword had some really funny parts, like when you break the chandelier and the wall of antiques. Oh, and Scrapper too!

They would just look at each other to see who got what he said and just attack him most of the time. He really likes to call the locals the peasantry in a way that's condescending but in a funny way. It's worth saving before a convo and trying the other dialog options to see how it plays out. There's alot of hidden humor scattered all over. I kind of perfer that approach over the pure comical games. Overexposure kinda numbs the funny bone for me. 

Idol Magical Girl Chiru Chiru Michiru is probably the game that made me laugh the most.

I'd vote for the Uncharted series, which has some great comedic moments...but does anyone remember the video game based on Harvey Birdman? I thought that was downright hilarious. I suppose it's very similar to Ace Attorney, but with the Birdman cast I was cracking up.

When your Fallout character has low Intelligence.

Kid Icarus Uprising and the Ace attorney Trilogy.

Conker was really funny from what I remember.