- As Morpheus, Trinity, and Seraph make their way to the MerovingianSeraph: There are no weapons allowed in this club. At the bottom of this elevator there is a coat check girl and, if we are lucky, a man to check weapons.Trinity: And if we're unlucky?Seraph: [deadpan] Then there will be many men.
- 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.
- There's some good Snark-to-Snark Combat between a few of the extras when the Hammer is rescuing Niobe and her crew."Want me to patch an uplink to reload your operations software, Sparky?""Yeah, that'd be swell. And could you clean the windshield while you're at it?"
- During the final battle, Agent Smith begins gloating over a defeated Neo, saying that he has seen this defeat before. He gloats about this before he breaks his own tone and mutters "I'm supposed to say something." And when he does pick his words, he actually winces and says "wait, what did I just say?" Long story short: Agent Smith's Villainous Breakdown is a very funny moment.
- Smith's frown, combined with his way of saying things like "I've ssssseen it" or "I'm jjust going to enjjjoooy the sshhhhhoooowww" causes his lower lip to come forward and rain to fall inside his mouth.
- Smith's last words sounding like a petulant child:Smith: Oh no no no no. No, it's not fair!
- "Cookies need love like everything does." Not to mention Agent Smith's goofy looking Evil Laugh after he absorbs the Oracle.
- As Neo negotiates a temporary truce with the Machines to confront Smith, the attacking Sentinels in Zion retreat.Niobe: What the hell are they doing?[Morpheus puts down his weapon and steps out of the shelter to watch]Niobe: What the hell are you doing?
- Roland's look after Niobe does an aerobatic 180-degrees followed by a shot of Rolland, who looks like he very nearly went into cardiac arrest: "Jesus Christ. I didn't know this ship could do that."
Funny / The Matrix Revolutions