- Johnny's intestinal problems.
Johnny: (after using the toilet) Wow, I didn't think that was possible! That's a record! Er... will this even flush?
- Big Boss falling in love with the first Cardboard Box of the series, and claiming that he feels at peace when he is inside of it, as if it was his destiny for him and the box to meet. What clinches it is Sigint's disbelief at Big Boss using the box as a means of camouflage and saying that he doesn't wanna know what he means when he says that he feels safe inside the box, promptly ending the conversation. Furthermore this gives a hilarious insight into why Snake (and even Liquid likes the box according to Super Smash Brothers Brawl) likes the Cardboard Box so much, it runs in the family.
SigInt: Uh... Snake? What are you doing?
Naked Snake: I'm in a box.
SigInt: A cardboard box? Why are you — ?
Naked Snake: I dunno. I was just looking at it, and suddenly I got this irresistible urge to get inside. No, not an urge - more than that. It was my destiny to be here; In the box!
Naked Snake: Yeah. And then when I put it on, I suddenly got this feeling of inner peace. I can't put it into words. I feel... safe. Like this is where I was meant to be. Like I'd found the key to true happiness.
Naked Snake: Does any of that make sense?
SigInt: Not even a little.
Naked Snake: You should come inside the box... Then you'll know what I mean.
SigInt: Man, I don't wanna know what you mean! Between you and Para-Medic, is everyone but me that is hooked up with the Major strange!?
SigInt: Yeah, well, anyway, I suppose even that dumb-ass box might make a decent disguise if you wear it inside a building.
- The Food codec calls.
- Snake nerding out on the customizations of his new 1911 pistol.
- At one point in the prologue, Snake sees a guard at the bridge. He looks up, notices a beehive up in the tree... and his face splits into a frankly hilariously wicked smile◊.
- The second time you meet Ocelot, he pulls some of the fancy gun twirling he'll be known for, then twirls it into his holster. Then pulls it out and puts it back in the right way.
- Zero geeking out over Bond.
Zero: Maybe if you changed your name to Double-O Snake?
- Sigint talking about a nightmare he once had where a giant turd shot turds at everything and turned everything into turds. The single most hilarious part about this is that it's actually fairly accurate Futureshadowing regarding Metal Gears as a whole.
- When Naked Snake asked if he could more or less make the first part of his codename true:
Naked Snake: So... Is there a way to take off my pants?
SigInt: Say what?!
Naked Snake: My pants. Can I —
SigInt: Aw, hell no! This FOX Unit is a nut fest!
Naked Snake: (cackles)
- Call Sigint after you get the Patriot to get this exchange:
SigInt: Where'd you get it?
Naked Snake: Hmm?
SigInt: I said, where'd you get it?
Naked Snake: SigInt, don't get worked up over details.
SigInt: Wha - ???
SigInt: ... and it never runs out of ammo?
Naked Snake: Never.
SigInt: Why's that?
Naked Snake: (sagely) Because the feeding mechanism is shaped like an infinity symbol.
- Metal Gear Raiden: Snake Eraser.
(Raiden teleports in, Terminator-style, and gets knocked out of the way by Naked Snake)
"You've created a time paradox! You can't go changing the future like that!"
(Raiden gets knocked into the air by a motorcycle, lands on top of Ocelot, whom he kisses by accident, and then starts dry heaving afterwards upon realizing it)
"You've created a time paradox! Don't mess with the future! You have to understand the future!"
(Raiden gets *ahem*ed by Volgin, resulting in the camera shaking off-screen as he's being... Roughed up. Yeah, let's go with that.)
"You can't do that! The future will be changed; you'll create a time paradox!"
(Raiden teleports to the scene where Volgin punches the oil barrel with Granin's corpse. Raiden is sent flying and the barrel lands over him. He then runs with the barrel on top of him.)
(Raiden teleports to the scene where Volgin beats up Snake for disguising as Raikov and ends up getting beaten up again by Volgin)
"You changed the future! You created a time paradox!"
[Raiden meets Big Boss in person during the chase scene with the Shagohod]
Raiden: The legendary... Big Boss...
- In the end, Raiden decided to go forward to the original Metal Gear and kill Solid Snake there, complete with actual 8-bit graphics. However, he gets shot by Big Boss, claims that he should have killed him when he had the chance, then the screen fades to black. The last line involves Rosemary saying that there will probably be a MGS 5. And sure enough, Raiden does return as the main character in Metal Gear Rising: Revengeance, salvaging something out of the sheer humiliation the poor guy had to put up with.
- The Secret Theater videos are all pretty funny! Sadly they were left out of the HD re-release though. Most notable examples including:
- Get Down! Sokolov gets someone else to save him. The hero is Sokolov in drag, with tons of Ho Yay.
- Payback: The DCI wants his handshake, dammit.
- Metal Gear S: Major Zero informed Snake that he will be joined by another operative, who turns out to be SigInt. SigInt handles most situations coolly and collected, while Snake always gets the worst of every situation.
- Gotcha This Time: Snake slams the butterfly-shaped C3 bomb too hard, causing the timer to reset to 0 and detonate the other charges, destroying the hangar. His expression is priceless!
- Die Hard Volgin breaks the laws of physics after the Shagohod unexpectedly crashes during the pursuit sequence.
- The Quick Version: Ocelot, demanding a final duel when chasing the WIG with his hovercraft. When he tries to jump in, he rolls to the other side of the interior, hits the opposite door, which breaks under his weight and sends him tumbling outside into the lake. As the screen blacks out, Snake gives a sigh of disappointment as he looks back after him. In the Japanese version, Snake mockingly says: "you're pretty good!"
- The Ultimate Weapon: The Boss and Naked Snake plays a serious form of Rock, Paper, and Scissors... it ends with The Boss losing and she certainly doesn't take it very well
- Cat-like Behavior: Just... see it for yourself.
- Try the conversation about the glowing mushrooms.
Naked Snake: Para-Medic.
Para-Medic: What's up?
Naked Snake: You were right.
Para-Medic: About what?
Naked Snake: I ate a Russian glowcap and it charged up my batteries.
Naked Snake: What's wrong?
Para-Medic: I, uh... that's... that's great! Um, Snake, can you excuse me for a second?
Naked Snake: Sure.
(She leaves her microphone. Snake can still hear her.)
Para-Medic: Did you just hear that?
SigInt: Yeah. There's no way eating a bio-luminescent mushroom would cause your batteries to recharge.
Para-Medic: What do you think it means?
SigInt: Beats me... maybe it's all in his mind.
Para-Medic: You mean like a placebo effect?
SigInt: Why not? You've seen how gullible he is.
Para-Medic: I guess there's no harm done. Should we let him keep believing it?
SigInt: Sounds good to me.
(She comes back)
Para-Medic: Okay, Snake, I'm back. Yes, the Russian glowcap is a glowing mushroom, so it'll recharge your batteries when you eat it.
- Talking to the people in your codec list (call Eva last) with the crocodile hat on shows you that the word "normal" does not apply to anyone involved with the FOX unit.
- The part when you rescue Sokolov. He follows Snake outside, imitating his MOVES, and somehow ending up with a Kamehame Hadoken gesture, at which point the camera pans over to Snake, staring at the scientist with a complete "What the frick are you doing?" look on his face.
- ALL the Easter Eggs in the third game qualify. Take your pick: between the conversation between Para-Medic and SigInt about Snake and the glowing mushrooms, calling Eva after you call everyone else with the crocodile head thing on, wear the scientist suit in the jungle, etc.
Naked Snake: What do I do if I meet that guy?
Major Zero: Beat the crap out of him.
- There's also this gem after you get Raikov's suit and call the Major.
Major Zero: Ah, your Raikov disguise has turned out nicely.
Naked Snake: Yeah. Not even his own mother could tell the difference.
Major Zero: Indeed. You're starting to irritate me already.
- The "Snake vs Monkey" minigame. Your only objective? Sneak up and capture the monkeys from Ape Escape.
- When you complete a mission, Snake does a cute little victory dance. When you finish the last one, Snake does his dance... while looking at a pin-up poster on the wall.
- The opening video. Just... that.
- The trailer for the 3DS version features a cameo by... Yoshi. Yes, really. And as of now, Yoshi replaces the Kerotan frogs in the 3DS version.
- On New Game+, if the player calls The Boss when Snake is wearing the Tuxedo or GA-KO camo, the following conversation occurs:
The Boss: Snake...
Naked Snake: What's up, boss?
The Boss: Don't you "What's up" me! Just what do you think you're doing?!
Naked Snake: Looks pretty good on me, doesn't it?
The Boss: Are you out of your mind? You can't wear that in battle! It's like saying to the enemy, "Hey, here I am! Shoot me!"
Naked Snake: Well, I'll admit, it's a little on the flashy side...
The Boss: Then why don't you -
Naked Snake: But it does look good on me, doesn't it?
The Boss: ...
Naked Snake: You don't think so?
The Boss: Listen, wise ass! Camouflage isn't going to do jack if it doesn't help you blend in with your surroundings!
Naked Snake: Well, I think it looks good on me...
The Boss: (exasperated) Fine! Wear whatever you want!
Naked Snake: (in the most dejected tone of voice possible) I - I thought you'd like it...
- Snake's thinking noises. Hm? Hrum? Grh? Guu? Gmm. Urh?
- Snake's reactions during long one-sided CODEC conversations. He gets so bored and just spaces out. Then asks how it tastes.
- At the conclusion of The End's Final Speech, his dentures fly out of his mouth in a gratuitous 3-D manner. Talk about Mood Dissonance.
- How can we forget, in the lead-up to the fight, one of his eyes suddenly popping out, Looney Toons style, to look through his sniper?
- One way to defeat him is to save your game and then let the system clock advance one week. When you resume, The End will be dead of old age.
- After escaping the jail cell, keep the transmitter in and go to the waterfall for a really funny hidden cutscene.
- In the HD remake, the achievement/trophy you get for killing Ocelot is called "Problem Solved, Series Over".
- Ocelot's meow, it's so disarming and anticlimactic.
- Zeixpe's Youtube videos of the game demonstrate an uncanny, perfect understanding of the game: Watch the insanity take place here.
- If you get a Dragunov early enough, you can snipe The End as soon as you see him in his first cutscene and skip his entire boss battle.....though you do get smacked by a wheel from his wheelchair after he explodes.
- During the conversation about vampire bats, Snake stops Para-Medic from talking about vampire movies. The examples he gives of B-movie titles include Attack of the Vampire Doughnuts and Dracula Versus the Space Hippos.
- If you throw a frog at Volgin during the fight, he'll actually stop fighting you and take a few seconds to focus all of his attention on the frog. The icing on the cake is this absolutely hilarious line:
Volgin: A tree frog!? Kuwabara. Kuwabara.
- Among Para-Medic's multitude of movie references, there's this gem:
Para-Medic: Hey Snake, have you ever seen 'My Mother was a Teenage Spider Queen from Mars'?
Snake: I can't say that I have...
Para-Medic: ... Neither have I.