Sam: What do I do with this? Jarvis: I'll give you a hint... Not that.
And in the lightcycle battle, Sam and a conscript manage to lure one of Clu's mooks into their trap. Sam rolls by the mook and says "Boo!" as the orange program looks at the user in confusion. Guess what happens a few seconds later...
While Sam, Kevin and Quorra are having dinner, Kevin asks Sam about his personal life. When Sam responds that he just has a rescue dog, Kevin responds: "Dogs are... dogs are cool."
In the same dinner scene, Quorra's outburst of laughter when Sam mentions he dropped out of college, thinking he was joking because she couldn't even conceive of any relative of Kevin not doing well academically. Meanwhile, Kevin and Sam just stare at her.
Also from the dinner scene, before anyone has said anything, things seem quiet and serious, until we cut to Quorra drinking her "Romulan Ale" drink with a very curious, wide-eyed, fixated stare on Sam.
The CEO's answer to Alan's question about the new edition of Encom's OS.
Alan Bradley: Given what we're charging students and schools, what improvements have been made in Flynn... er, I mean, Encom OS 12? beat CEO:(who has no real idea) ... Yeah, this year, we put a "12" on the box.
Sam is on a first-name basis with the impound lot attendant.
Sam: Hey Carl!
Carl: *Sigh* Hey Sam!
Kevin Flynn was apparently cool before cool was cool:
Kevin Flynn: What's Wi-Fi? Sam: Wireless interlinking. Kevin Flynn: Of digital devices? [Sam nods] Kevin Flynn: Heh. I thought of that back in '85.
The exchange on the Encom rooftop after Sam stole the OS-12 and put it on the internet for free.
Sam: Don't sweat it, your boss is ok with it.
Guard: Yeah, the hell he is!
Sam: Your boss works for the CEO. And the CEO works for the shareholders. Now, do you know who the biggest shareholder is?
Guard: I dunno, some kid.
Sam:*gestures at himself*
Guard: *In disbelief* You're Mr. Flynn?
"I have a three-inch version of you on my shelf!" [gets disc hurled at him] "It definitely didn't do that!"
When Quorra is rescuing Sam in the Light Cycle grid, she goes to make the big jump out of the arena. Sam screams that they won't be able to make it, but she simply engages the modified engines and makes the jump, then adds a smug little "Made it." The kicker is the little shake of her head she makes as she says that; even with the helmet concealing her features, you can see the grin she's gotta be sporting.
Clu and Jarvis poking around Kevin's home, not sure of what to make of all the little elements of the real world that he has scattered around his home, like his books or chandelier. Particularly when Jarvis knocks over some glasses, and stands there frozen like a startled deer.
The whole scene where Sam tries to get his dad updated on the real world (Lakers vs. Celtics, his bike, etc.)
Sam fumbling with his disc when it bounces back to him.
In a Blink And You'll Miss It moment just before Sam enters the Grid, he does a quick history check on the laser's console. Most of it pertains to the functions of the laser system, but one single line reads: "sanity_check"
Quorra's dorky, snorting laugh.
The film does not have to be in the computer for all the humor to happen. Remember that taxi that Sam landed on after jumping off the tower?