Anytime Jack and Stark snip at each other is a moment of funny.
Nathan Stark: Yes, he said "invisibling".
While Stark was technically an illusion. It was still pretty funny to see them snip at each other again.
Jack: I just don't get it. (Behind him, Stark is suntanning)
Stark: It's science, Carter. No one expects you to get it.
Jack: Well, if it's... (sees Stark) Put a shirt on!
Stark: Hey, this is your fantasy, not mine.
"Purple Haze" and that's all I'm gonna say.
Jack: You're naked!
Taggart: Au natural.
Jack: May I ask why?
Taggart: Why not?
When Jo's first getting used to her new P.A.L.s in "Glimpse" (contacts which predict the future, essentially), Carter points out that nothing is better than a cop's normal gut instinct. He tries to demonstrate while Jo's P.A.L.s identify the funny accident which is about to befall him. She says nothing. So naturally, he gets covered in lamacoid (banana slug) juice... FUN!
When Jack is about to go stop a swarm of rampaging nanobots.
Jack: How hard can it be to stop a mindless eating machine?
Alison (who is pregnant): You looked at me again.
Jack and Henry are speculating as to how and why a bunch of people from the 21st century ended up in Camp Eureka, 1947.
Jack: Tess was telling me about massive solar flares that were putting out lots of negative energy, ironically just before she dumped me.
Henry: I think she's right.
Jack: Well, that's not very supportive.
Henry: No! About the flares!
Fargo's explanation to Joe about why he's not wearing any clothes.
Fargo: (worst Arnold Schwarzenegger impersonation ever) Your clothes, give them to me, now!
The episode "This One Time at Space Camp…" has poor little "relationship auditor" Warren Hughes get zapped by some tech. Then he starts running around thinking he's Jack. Warren's now reliving moments of Jack's life as if it were his.
Also from that episode.
Mr. Hughes: What were you expecting, the Spanish Inquisition?
Poor little Holly during her interview with the committee can't stop thinking!
The entire 2011 Christmas special
Jack: I HAVE A HAT?!?
Jack: Did my jeep just yell at me?
Later, The fight with Ninja Snowmen!
Jack: Back off Frosty!
rapid Art Shifts, including Peanuts, Simpsons, South Park, and Scooby Doo.
Finally: the Anime fight at the end. Easily the most Crazy Awesome moment in the show.
Jack's cry of joy when he's told that someone has robbed the bank. Then he discovers that someone has actually ripped the bank from the ground and pulled it elsewhere.
In the Season 4 finale "One Giant Leap" Jack has recently discovered how to work the phone that has always been in his PDA that he never knew about. The Disaster of the week starts to combine into a Eureka-consuming Black Hole and everyone is running for their lives. What's Carter doing? Taking pictures the whole way. Fridge logic later on when he's reviewing the images and it takes a minute of scrolling to find the one he needs.
Fargo walking out of a lab (that's on fire) all smiles as his left pant leg burns. Subverted slightly when he mentions Holly as if nothing had happened to her.
The entire scene in "Jack of all Trades" where Zane pulls someone over for speeding while he is in Jack's body. Actually, that whole episode was pretty funny.
Colin Ferguson (Carter) and Neil Grayston (Fargo) do an excellent job of pretending to be each other.
Henry accidentally lets slip that humans have been to Mars.
Jack: We've been to Mars?!
Henry: (While nodding) No.
He does this again when Jack asks if Area 51 exists.
After it's revealed that S.A.R.A.H. started her/its existence as a war-game simulator: