Overall, I'd go with the conversations between Joker & EDI.
"Oh, Joker was such a tool. I have to spend the whole day computing pi because he plugged in the Overlord." Later on, when EDI says he has to crawl through the vents. "I like watching humans on their knees, Mr. Morreau." *Joker stands stupified.* "That was a joke, Mr. Morreau."
Talli and Garrus in the Citadel, [url="http://www.youtube.com/watch?v=0a54Vm1ww8w"]reminescing about the elevator rides.[/url]
Finally, a lot of the funny stuff was in the background conversations, like the man & woman you helped decide on gene therapy for the woman's child. "What are we going to buy?" "Maybe I should ask some random stranger walking by." Or the Turian who's making a pass at the Quarrian in the Eternity bar on Illium. "You're better off with someone else, someone who you can share your food with."
Feel free to add.