Obi-Wan's amusing yet morbid Call Forward remark: "Why do I have the feeling you're going to be the death of me?"
Anakin's "Not again," when his lightsaber is destroyed. Which becomes something of a Brick Joke later when someone apparently expected this to happen, as they brought him a spare.
The way he finds out about his lightsaber. He comes up ready to fight and beings his weapon up-only to see that it's cut in half.
The entire sequence where Yoda has the class of Padawans explain to Obi-Wan why information on Kamino is missing in the Archives. The tone of his voice obviously suggests that what he means is, "Figure it out, these kids can. Slowing you down, what is?"
Also, his very amused "Lost a planet, Master Obi-Wan has. How embarassing." The children all giggle in response, and that single scene makes it clear not only how good Yoda is at training, but how much he enjoys it.
Obi-Wan uses the Force to open what was earlier established to be an automatic door.
When Anakin and Padmé are being chained up next to Obi-Wan for public Roman-style execution, Obi-Wan gives Anakin a death glare and Anakin responds thusly:
Anakin: "Then we decided to come and rescue you." Obi-Wan: *beat* "Good job."
The expression on Obi-Wan's face as he says this (right after glancing up at his chains and then looking back to Anakin) is a hilarious mix of sarcasm, false congratulations and frustration.
At the start of the arena fight in Episode II when Padme climbs the pillar:
Anakin: What about Padme?
Obi-Wan: She seems to be on top of things.
As Anakin and Padme have their first kiss at the lake house a soft version of their love theme plays. When Padme quickly breaks it off the music also cuts out! Also Anakin's face afterwards like he's thinking "What the hell?!"
In the documentary "From Puppets To Pixels" included on the special features, George describes Yoda as the "illegitimate child of Kermit The Frog and Miss Piggy."
C3PO gets his head separated from his main structure, and fused onto a battle droid's body:
"DIE, Jedi dogs! Oh... what did I say?"
Also from that scene:
"I'm programmed for etiquette, not destruction!"
And the battle droid's reaction:
Kit Fisto defeating the battle droid 3PO, and grinning before jumping back into the fight.
This begs some explanation. Fisto Force-shoves 3PO over, and 3PO accidentally shoots a super battle droid in the back, which causes it to fall on top of him. Now wonder why Fisto was grinning.
Then R2 shows-up to save 3PO: he attaches a cable to his head, and despite 3PO's complaining pulls until the head comes off the battle droid's body, then brings the two pieces together. What makes this particularly funny is 3PO's puntastic commentary:
C-3PO: Oh, this is such a drag.
C-3PO: I'm quite besides myself.
During the Arena battle, Anakin and Padme take cover in an overturned chariot and engage in some Casual Danger Dialogue. Padme goes straight from delivering a Call Back one-liner, with a flirty look on her face, to having this horribly distressed look on her face as she goes back to shooting at the enemy.
While C3PO is suffering comically, R2D2 gives a beep that can only mean "Great, I have to save his butt again."
Towards the end, as Anakin saves Obi-Wan from a finishing blow by Count Dooku, moments after he was struck by his Force lightning.
Dooku: That was brave, boy, but foolish. I would have thought you'd have learned your lesson.
Anakin: I'm a slow learner.
Also, Yoda transforming into a Tasmanian Devil-caliber spinning bouncing whirlwind of lightsaber fury for his duel with Count Douku... and then picking up his staff afterward and shuffling away like an enfeebled old man.
Fridge Brilliance: He is an enfeebled old man. Drawing heavily on the Force is what lets him become that tiny whirlwind of lightsaber destruction. After the fight, he doesn't need to keep drawing on the Force like that, and may actually be wearied from it, his body complaining at what it was just asked to do.
At the start of the execution, a Nexu jumps at a Geonosian picador off his orray, and maws its head. The crowd cheers for that.
The film's website listed information on the film, including who the characters were. They also had pictures of these characters, but used their appearance in the original trilogy if their images from the film weren't ready to be shown yet. Bail Organa's picture from the original trilogy? The destruction of Alderaan.
When preparing to film Dooku and Yoda's lightsaber duel, George Lucas and few others wheel out a Yoda maquette. . . with giant fake vampire fangs pasted on the mouth. How does Christopher Lee respond? A weary "Oh, George. I didn't think you'd do this to me."
When Anakin and Padme have their Big Damn Kiss, they're being carted out into the arena and only break it off just as they get out of the door. Obi-Wan is standing about thirty feet away. He almost certainly saw that kiss, which makes his silent "what the hell?" look to Anakin as they pass even funnier.