In "Chicken Jack", the only reason that the spell cast on Jack wears off is because the moody wizard flew off the handle upon the cock fighter manager bumping into and accusing said wizard of not watching where he was going. The spell reversed Jack's condition, but turned the manager into a chicken himself. The confused look on said wizard really sells the whole bit.
Also what comes immediately afterwards:
Vendor: Welcome back. The chicken again?
Jack: NO!NO CHICKEN!! (Pounds the counter and sends a spoon flying) I mean, I will have the shrimp instead.
What makes it even funnier is that Aku keeps trying to stab Jack even after it failed the first time and as he screams "How!?", his eye-brows start to grow back.
There's one moment in "Jack and the Hunters" where Jack, cornered by the Emikandi, runs into a nearby ambiguously tall building, and discovers an orange button with an arrow pointing upwards. Figuring out what it's used for, Jack presses the button, and the room he's in starts to move up (turns out it's an elevator). This forces the Emikandi to follow him into the next available elevator and pursue him in a hilariously long, silent chase sequence where Jack continuously foils the Emikandi by getting off his elevator and simply walking into another.
The entire of the episode "Aku's Fairy Tales", which focused on Aku's brand of storytelling to a group of young children:
(Cut to Jack's baffled face as a goofy sound effect plays)
Jack's goofy smile right before he realizes he's been had in the first act of "Jack's Tales".
"Jack is Naked", especially when he has to dress as a princess.
The entirety of "Jack's Sandals" The highlight is when he wears a pair of Combat Stilettos, only to have the bad guys hit on him.
Most of Jack's interactions with the Scotsman. Most notably when they're challenging each other at contests to see who gets to row the other back home from a remote island. It all comes down to an epic battle of thumb wrestling.
In the episode where the Scotsman goes on a boat and discovers that Jack has lost his memory, Jack talks like a Totally Radical surfer dude.
The final interaction between Jack and the Scotsman's wife:
Jack: It appears we will have to find another way out. Scotsman: What's wrong with this door? Jack: Well, you see: The door is so very small, and your wife is so very — Scotsman's Wife: WHAT?! (Jack realizes what he just said) Scotsman: RUUUN! (Jack bolts away out the tower, the Scotman's wife close behind) Scotsman's Wife: LA-LA-LA-LA-LA-LA-LA-LA-LA-LA-LAAAAAAAAAAAAAAAAAHHH!!!
Jack, disbelieving what Aku just said, then proceeds to swing his sword at him, Aku turning into a bat form, fleeing, yelling, "I'll be back, samurai! You'll see! HAHAHAHA!" He flutters away for long enough that Jack starts getting thoughtful before turning back and saying "See what I mean?"
Not to mention, they go through this routine again at the end of the episode.
The way the episode begins is hilarious, with Aku speaking on a land-line telephone to get minions to attack Jack. It sounds like he's ordering a pizza.
Aku: Yes, I would like to place an order for delivery...Aku...I think I'm in the computer...Yes, that's it! I'd like large - huh, what? ... Extra thick! ... Thirty minutes or it's free? Excellent!
How about when Aku's minions try to destroy Jack?
Round 1: A ogre like minion practically five times taller than Jack is the first to arrive. He roars, Jack merely jumps up and slashes. Cue *boom* and Aku commenting on how stupid that was.
What was really funny about the scene. When Aku told the first minion to destroy Jack, the minion roared, then split cut later then minion is driving car that was too small for the minion. The minion drove the car right up Jack and then the minion smashed his way out of the car.
Round 2: A giant robot begins extending a chest cannon so long it's basically no bigger than a gun barrel when it's fully extended is only less than a meter away from Jack as it fires... a pea-sized shell which just bounces off of Jack's sword. Cue Jack staring in surprise and the giant trying to regain its former standing posture only to slip, fall and blow up. Aku comments on how stupid it is. Again.
Round 3: A huge robot army armed with steel blades and shields march towards Jack as he prepares his stance and fight them off. Cue one of the robots tripping, sending its blade flying through the air and onto another robot, leading to it exploding, destroying and damaging the ones around it, causing their blades to fly off and repeat the chain reaction. This eventually leads to only one bot remaining as it gets near Jack who is still maintaining his stance... until another blade ends up on the last robots back and destroys it. The explosion is just strong enough to blow away Jack's hat. This earns another 'stupid' comment from Aku.
Also good is when Jack has to ask for clarification on where the duel will take place.
Aku: We shall meet before the rising sun at the ancient ruins beyond the Valley of the Corpses. Jack: Agreed... was that east or west of the Crimson Hall of the Ogre? Aku: East. Jack: East, right... Aku: You know where that is? Jack: *beat*... Yes, yes I will find it. Don't worry. Aku: Are you sure? Jack: No, no. Don't worry. I remember now. *averts his eyes in thought* Aku: ...I can give you a ride if you— Jack: I will find it!
Then a moment or two after that we have several cuts back and forth of Jack and Aku just staring at each other awkwardly, before Aku smiles, and Jack responds with the most forced and awkward looking smile ever.
Pause at the very beginning of the portal sequence in the intro. Look closely at Jack's face. Try and hold in your laughs.
The first episode of season 2, "Jack Learns to Jump Good", opens with Jack having just fought his way through a horde of Aku's drones to reach a time portal, when Aku suddenly appears and snatches the portal away. Aku then proceeds to dangle the time portal just beyond the reach of Jack's jump and giddily watches Jack hopping up and down trying to reach it.
Compare it to the end of the episode, when Jack uses his new jumping skills to his advantage.
Aku: Samurai fool. Your efforts are in vain again. This gateway into the past is once more (Jack springs far into the air) beyond your reaaa- YOU CAN FLY!?! Jack: No. Jump good.
The Scotsman's wife yelling at him while he just stares at her with the most absolutely lovestruck expression ever. Jack looking back and forth between them in confusion is gold.
Whilst "Jack and the Lava Monster" (X) is mostly known for its Nightmare Fuel, there's one line early on that's just too much, especially thanks to Jack's usual demeanour:
Jack: Surely he takes me for a fool to follow deeper into his trap. (Spiked ceiling starts to lower) Jack: A fool I be! (Races deeper into the maze)
When Jack breaks Da Samurai's masquerade, he gives them most appropriate confused look ever.
Scotsman Saves Jack has a number of highlights. On of note is when the Scotsman is trying to look for people that remember Jack, he breaks into a bar and screams "Has anybody hear seen this man before?!" The whole building turns out to be full of bounty hunters and that Scotsman then beats the crap out of them. Later when Jack and the pirates start getting entranced by the Siren's song, we see everyone with Hypno Eyes, except the Scotsman, whose annoyed and says "Sounds like someones step'en on a cat. Sounds like someones stepp'en on a lot cats."
In "Jack, the Monks, and the Ancient Master's Son", Jack freaks out when he thinks that he has led Aku to the secret Shaolin temple, but the Grandmaster calmly points out that he shields the temple from Aku's gaze with his connection to the earth. Cue Aku staring angrily at his viewscreen, which is now covered in television static, and banging on it as one would a malfunctioning TV. It's also Aku's only scene in the whole episode.