When Jed and Octavius are popping Cecil's tires, and they get blown away by the violent gush of air coming out of the vent. Made funnier when the scene cuts to a Distant Reaction Shot of the van from a normal person's perspective that shows an almost inaudible sound being made as the air is released. They do the same thing in the sequel when Octavius is comandeering a squirrel and trying to ride it to the White House, and then we see just how far he has to ride it.
Atilla portrayed as a a huge fussy child with anger problems equals comedy gold. The scene were Larry manages to connect with him and the Huns is both funny and heartwarming.
Dr. McPhee in general, but especially when Larry has to explain himself the next morning for humorous positions that the miniatures froze in:
McPhee: Whahahahaha. Let's all laugh at me, the comedy night guard. No, is the answer. Sarcasm, back at you, with your humor box. I wasn't laughing. I was pretending to laugh, if that's what you want, some sort of battle of humor. Do you? Larry: No? I don't want a— No, I don't want a battle of humor. McPhee: No, you don't, because it would be a bloodbath. Nothing funny about Little Bighorn. No. I find it about as funny an a fancist... It's not funny. Okay? And I will not stand for this type of blatant ssss.... If I'm not clear, tell me. (Beat) Am I clear? Larry: Yeah? McPhee: Yeah.
Or this bit when he reluctantly decides to give Larry one last chance:
McPhee: And if anything, the tiniest... after your shift... (smacks his hands together and makes a smashing sound effect) Because... Larry: Got it. McPhee: Okay. Fool me once, shame on you. Fool me twice... Larry: Shame on- McPhee: Huh? Larry: Fool me... Shame on me.
Battle Of The Smithsonian
Kahmunrah's dismissal of Darth Vader as an incompetent villain because he's an "asthmatic in an opera cape".
Also, the moment when Kahmunrah kidnaps Jedediah.
Kahmunrah: (to Jedediah) I'm sorry, but I can't take you seriously, even when you're threatening me! You're just adorable!
Plus the whole part where Larry and Kahmunrah try to negotiate over Larry's friends and the tablet. A highlight:
Kahmunrah: All right, I'll tell you what. They didn't call me Kahmunrah the Trustworthy for nothing, all right? (starts to hand Larry the hourglass with Jed in it) Here you go... (jerks it back) They didn't call me Kahmunrah the Trustworthy! They called me Kahmunrah the Bloodthirsty, who kills whoever doesn't give Kahmunrah exactly what he wants in the moment that he wants it, which is right now, when I had also better get the combination and the tablet!
Larry Daley: ... That's what they called you?
Kahmunrah: It was shorter in Egyptian.
Also from the same scene: "This is a no touching zone!"
Kahmunrah I am Kahmunrah, I am half god, once removed on my mother's side.