There are 2 that deserve to be at the top of the list for their timing and brilliance.
1) "The Big Lewbowski":
"Phone's ringing Dude"
That exchange is done with such perfect comedic timing that it still makes me laugh thinking about it.
2) "The Sure Thing"
The entire premise is about this school kid traveling to California to meet "the sure thing" and how he falls for a different girl along the way. At the end of the movie, he is reading to the class about his adventure as a school project. When he gets to the part about meeting the "the sure thing", he says that didn't go through with it, at which time in the back of the room you hear quietly "Traitor".
The traitor line reflected what most guys were thinking as well and the way they quietly slipped that response in the background was awesome.
"Get 3 coffins ready... I don't think it's nice, you laughin'. Ya see, my mule don't like people laughin'. He gets the crazy idea you're laughin' at him. Now if you apologize like I know you're going to, I might convince him that you really didn't mean it... My mistake, 4 coffins."