A very sly one, when Link comments that the earth appears to have warmed up, stating that it is 'a convenient truth'.
We have another when Monger shows videos of the monsters at Area 52. After he says the name of one monster, the coffee lady screams in terror, every single time, to the point where Monger can't take it anymore and asks someone to get her the hell out. Then he finishes by introducing Ginormica, and we hear another female scream. It was the President.
The scene on the the spaceship where B.O.B., upon receiving a gun and pretending to be part of the invading army, accidentally activates the gun and kills a goon- it's not so much what B.O.B. does but the expression on his face when it happens- you can almost hear him thinking oh look a dead goon, COOOOOOOOOL...
The line leading up to that moment. The delivery is just so absolutely perfect.
Gallaxhar's recounting of his origin, and the destruction of his planet. As it's told while he's going through the cloning machine, it cuts him off every few seconds. And because he doesn't seem to realize this, we're treated to a few random details that are downright hilarious, starting with a horrible secret from his parents, encountering a giant (blank) after leaving home, shortly thereafter being married to someone, and then having marital trouble. By that point, he's decided that Susan knows too much, completely missing the look of utter confusion on her face.