This scene. It's a total curbstomp, and the guards don't see it coming at all.
Neo walks through a metal detector and it goes off. Guard: [coming over to Neo with a tray in hand] Would you please remove any metallic items you are carrying? keys, loose change... [Neo opens his trenchcoat to reveal enough guns to kill a small city] Guard: Holy shit! [Neo strikes him hard enough to send the guy flying backwards. As the other lobby guards look up, Neo whips out twin automatic submachine guns and fires them in both directions, spraying them with bullets. One guard dives for cover] Last Guard:[on radio] Backup! Send backup! [A beep is heard. He looks up and sees Trinity come through the metal detector. The guard tries to draw his service revolver, but she raises a submachine pistol and shoots him]
"Morpheus is fighting Neo!" *everyone rushes out of the room, one of them leaping over the table*
Neo's conversation with Smith after being arrested.
Neo: That sounds like a good deal. But I've got a better one. How about I give you the finger, [he does so], and you give me my phone call?
Not to mention Smith saying "Hmm.." when Neo flipped him off.
After Neo finally defeats Smith, the two remaining Agents look at each other and, by wordless agreement, execute a simultaneous Screw This, I'm Outta Here!.
The Oracle: You're cuter than I thought. I can see why she likes you.
The Oracle: Not that bright, though.
The way Agents Smith, Brown, & Jones say everything in a very sinister, machine-like way (putting stresses on the wrong syllables, adding pauses in inappropriate places, and elongating their s's) can lead to a bit of humorous Narm Charm.
Agent Smith: You have a social security number, you pay your taxes, and you...[looks up dramatically]...help your landlady carry out her gar-bage.
His >_<-esque facial expression after the line makes it even funnier.
"Come on, stop trying to hit me and HIT ME!"
After Neo and Trinity blow the ever-loving shit out of the ground floor, Agent Jones and Agent Brown confront Agent Smith with the news ... right as the sprinklers come on and soak the Agents.
Neo swiping a phone from a bystander during the climactic Run or Die sequence. "What the shit—THAT'S MY PHONE!"
When Neo tries to escape, Tank tells him to go to the door on his left... and he goes to the door on his right. "No, Your Other Left!"
The DVD Commentary with the special effects guys and part of the cast has this. They apparently had a mid-wrap party when the opening sequence was done and had Trinity's introduction playing on a TV, which her actress had them replay again and again as she had more to drink throughout the night.
Morpheus's Casual Danger Dialogue when he first contacts Neo, when he tells him to look at who's coming for him.
(Neo peeks above his cubicle to see the Agents, who look in his direction and he scurries back out of sight)
Neo: You ever have that feeling where you're not sure if you're awake or still dreaming?
Choi: All the time; it's called mescaline. It's the only way to fly.
When Neo finally realizes his powers, he's initially dazed by this and is so stunned that when Smith tries to engage him in combat again, Neo isn't even paying attention, including parrying Smith's flurry with one hand while he takes a moment to the side to let it sink in. Then when he destroys Smith, he comes to and stares down the remaining two Agents, who look at each other and immediately high tail it.
What really sells it is that when Neo is blocking Smith's attacks with one hand, he actually turns to face away from him and casually holds his other behind his back while putting on an expression of complete and total indifference.
The Merovingian: I have sampled every language, French is my favourite - fantastic language, especially to curse with. Nom de Dieu de putain de bordel de merde de saloperies de connards d'enculé de ta mère. It's like wiping your ass with silk, I love it.
If you don't know French, plugging his French phrase into Google Translate and discovering what he's actually saying is... enlightening: " Damn damn fucking shit fucking assholes to motherfucker," or if you actually speak proper French, " Name of God of a shitty whorehouse of slutty idiots screwing their mother's assholes."
He uses this line twice: First just to show off, then later, when he discovers Persephone's little betrayal, as an actual expletive!
The Merovingian showing off his theory regarding choice by illustrating a program he's written: a piece of cake laced with signals that causes the eater to have an orgasm, complete with a Matrix Raining Code zoom between the woman's legs as it goes off.
Persephone telling the mook that The Merovingian is in the ladies room.
Trinity's less-than-enthusastic reaction to Persephone's trade of information for a lover's kiss.
Persephone: Just a sample.
Trinity: *whips out gun* How would you like to sample this?
The Merovingian's Angrish-bordering French rant when he learns of Persephone's betrayal, then denies he's wearing lipstick from the woman he was just with.
Persephone: She wasn't kissing your lips, my dear.
And then when Neo stops the hail of bullets from his henchmen:
Merovingian: Okay, you have some skill.
When Neo curb-stomps the Merovingian's mooks.
Merovingian: Goddammit, woman, you will be ze end of me.
Smith's face after the back-alley brawl between Neo and the dozens of Smiths. Hugo Weaving's many faces of disappointment have to be seen to be believed. And each and every one of them is guaranteed to make you lose your shit laughing.
The fact that they, after the above, all look at each other and start dispersing in a "Nothing to do here." kinda way.
One of the Smith clones is twitching his nose, as if he'd taken a particularly hard punch to it.
Also during the actual brawl, when Neo is thrown into a crowd of Smith's he knocks them over to the sound of dominoes falling. Later when he does the same to a Smith, they fall down to the sound of bowling pins being hit.
Link, when Neo gets transported to a different location in The Matrix when trying to escape the Merovingian's stronghold:
(Neo opens door to find he's in a mountain range and calls Link for his location)
Link: You're not gonna believe this, you're all the way up in the mountains.
The Architect's endless TV's show all possible futures. At one point, they show endless variations of Neo Flipping the Bird, insulting him, threatening to beat him up, etc. A few minutes later, they simultaneously scream, "BULLSHIT!!!"
Link's wonderful suppressed dirty words when he see Dozer's children in the room with Zee.
Link: (to Zee) "Where's my puss... (sees the little kids) Heyyy......"
Trinity starts asking Link for a program to wire a motorcycle... and the Keymaker gives her the key for the cycle before she can even finish the question.
The Twins's almost-bored Casual Danger Dialogue during the action sequences: "We are getting aggravated." "Yes we are."
Twin: (to his other counterpart while getting his arm shot over and over) Can we move along?
During the back-alley brawl, an Agent enters the simulation to fight Neo and the rampaging Smiths, only to be stopped by another Smith. We then get this priceless exchange:
Smith: Yes, me.
The Smith sticks his hand into the Agent's chest and starts to infect him
Smith: Me, me, me.
The Agent finishes transforming into a Smith and looks at the other Smith
Smith 2: Me, too.
The Matrix Revolutions
The Merovingian's response to Trinity, Morpheus, and Seraph breaking into his club and making their way across the floor in a three-way Back-to-Back Badasses formation, pointing their guns at everyone.
Merovingian: What in ze hell?
The end of the exchange between the Oracle and the Architect at the end of the film.
The Oracle: Do I have your word?
The Architect: What do you think I am? Human?
The Mega-Slow-Mo-Close-Up FALCON PUNCH. This is the absolutely least appropriate moment for such a scene, but I dare you to look at Smith's contorted face and listen to that drawed out "UUUUAAAARRRRGGGGHHH" without splitting up.
Path Of Neo
"Mega-Smith", as the game calls the Final Boss, is composed of bits and pieces of the destroyed city, and looks remarkably similar to the real one even though he's not wearing his Cool Shades. Mega-Smith then looks to his right to a billboard conveniently advertising shades, takes the giant shades, and puts them on, completing the ensemble and smiling.