Snake flirting with Mei Ling the instant they meet. "I can't believe I'm being hit on by the famous Solid Snake!"
Mei Ling: I'm surprised. You're rather frank for a trained killer.
In the Briefing videos, Snake is annoyed that he was stripped naked to make sure he didn't have any weapons. When he mentions it over CODEC, Naomi flirts with him in response (which becomes very ironic later).
Naomi: Well, if you come back in one piece, maybe I'll let you do a strip search on me.
Snake (smirking): I'll hold you to that, doctor.
Psycho Mantis saying the games Solid Snake—no, the player likes! It is also one of the Easter Eggs found before your fight against him, along with the photos of the developers behind him. And certain versions, if they read save data for Snatcher or Policenauts, rewarded players with a message from Hideo Kojima himself!
Twin Snakes also modifies the commander portraits in Mantis' boss fight room to that of Silicon Knights CEO Dennis Dyack, cutscene director Ryuhei Kitamura and, of course, Mr. Kojima. They all begin laughing at the player too. At one point, Mantis seemingly sets the room on fire, including the portraits. Poor Dyack gets reduced to a charred skeleton while Kojima...looks at him with mild interest.
Try calling Mei Ling repeatedly and refusing to save. The look on her face when she realizes Snake is screwing with her is just priceless. It ultimately results in her poking her tongue out at Snake.
Calling Nastasha while having weapons and gear equipped will have her give you some helpful information about them. Call her while you're hiding in a cardboard box, and she'll give a much longer and ludicrously well-detailed spiel about corrugated cardboard's history, construction, and its many practical applications, all with a completely straight face. Additionally, calling her while smoking leads to one of the few times someone talks with Snake about cigarettes while not rebuking him for smoking (take a good look at the smoke Nastasha's equipped with). Apparently compared to the dangers of nuclear...anything, Nastasha just sees smoking as the lesser of two evils.
If you call Miller while on a noisy floor, he'll give the player advice for sneaking around in real life. In a nice riff on the PlayStation's lack of finer analog stick control, Snake then remarks, flustered, that he literally can't do what Miller advised (Twin Snakes omits this bit and simply has Snake acknowledge the advice, referencing the GameCube's improved control stick tech and Snake's ability to walk slowly). Then Miller suggests that Snake put his socks over his shoes - or just crawl.
This gem just before Snake's fight with the Cyborg Ninja:
Not to mention Otacon pissing himself earlier. He pisses himself twice in the remake.
Near the end of their conversation Snake suddenly asks Otacon if he's feeling well. Otacon is confused by his sudden friendliness, especially after Snake throttled the poor scientist off the ground minutes ago. Snake awkwardly explains he's just nervous because the last two people he rescued suddenly died in front of him.
An unintentional one (but that probably makes it even funnier): if your health is low enough, Meryl can slapyou to death.
The Twin Snakes is filled with both Narm and intentional over-the-top humor. One moment is when Snake pitches a grenade like a baseball down the tank's gun barrel, sending a flaming soldier ragdolling away from the wreck. Said soldier lies on the ground for a few seconds, on fire, then gets up and begins screaming and rapidly patting at the flames before Snake punches him out cold.
Just as funny is Snake's reaction to Baker forgetting Meryl's frequency: from grumbling "damn." and annoyedly thumping his knee in the original to flailing about and pointing his gun at Baker in blind rage in TTS.
In the infamous scene in TTS, when Snake jumps off the Hind's missile to shoot his own, when it connects, we quickly cut back to Snake, who falls on his neck as the Hind spirals out of control in the background.
When Meryl asks Snake how he recognized her under the disguise, he bluntly responds with this:
It gets even better afterwards in TTS, where Snake's next line about how "on the battlefield, you never think about what's next" has a noticeably-longer pause between the end of the line and the scene fading out. You can just feel him regret saying it.
If you fail to follow Meryl's footsteps across the small minefield, and set off a mine, Meryl will shrug her arms as if to say, "Well, I tried."
In Twin Snakes, after the first Sniper Wolf fight and Snake is captured. One of the grunts tries to knock him out from behind. It doesn't seem to have any effect beyond just angering Snake, he turns to the grunt who backs off fearfully... before Snake drops like a ton of rocks. Moments before that, after Snake tells Wolf "I'll die after I kill you", one the guards gets closer to Snake to intimidate him, only for Wolf to casually backhand the guard with her gun. The poor guy recovers a moment later, shaking his head to compose himself.
In the scene before the torture mini game, Sniper Wolf in the remake tries to seduce Solid Snake by caressing his body, only to get frustrated that he isn't reacting. Not a moment later, Ocelot leans in expecting a kiss from Wolf, which grosses her out and she storms out of the room.
Ocelot also does a Fourth Wall banger to the player during the interrogation stage. The Twin Snakes had Ocelot specifically point to the camera during this, to add to it.
Ocelot dropping his revolver while trying to twirl it with his left hand in The Twin Snakes. Especially with how he just stares at Snake for a second before picking it back up.
Even funnier when you remember that in both MGS2 and MGS3, the latter taking place decades before this one, he was spinning a gun around with his left hand without an issue in most of his appearances, so this was a legit clumsy moment from Ocelot.
While in jail, you could do anything you can think of to annoy the guard. "Shut up in there, will ya!!!"
Also, "(What) the hell are you doing?"
If you call Snake's codec team after interacting with Johnny, you'll hear Snake talk with a cold. The original even has Snake sound very, very congested.
In one of TTS' briefing videos Snake is offered a smoke, and Naomi spends the duration of the footage trying to take it off him, finally succeeding right at the end and stomps it flat.
Some of the things Master Miller says becomes funny in hindsight, after you know that Miller is Liquid in disguise. Such as advising Snake to "wear a hat" to keep his head warm, or telling Snake flat out, "If all else fails, call Campbell for advice".
Sooner or later, the player realizes that half of Miller's advice is aimed at the player themselves rather than Snake. He states that gaming after a bath or on a full stomach should be avoided, or to be prepared to sit in front of the TV for a while if a long demo comes on. It becomes hilarious when you wonder just how well that's going to help Snake in his current predicament.
Codec talk, before Hind battle:
Campbell: It looks like Liquid wants to have a showdown with you. I'm looking at Mei Ling's digitally enhanced satellite images right now. Naomi: Snake, he's waiting for you. He's just circling around like a buzzard. Snake: I hope everyone's enjoying the live broadcast?
Call Nastasha during the Hind D battle, and she'll give you advice on how to use the stinger missiles. After that, she caps it off with, "Now shove that stinger missile up his butt!"
The crew advise you to use the speakers on your TV to listen for where the Hind is coming from...unless the player doesn't have one or has the sound set to Mono. Then they're aghast that Snake doesn't have a stereo TV, before Campbell tries to reassure Snake he's not a lesser man for not having stereo sound output, in the same way a teacher would reassure a sad kid!
Campbell: Snake, don't worry about it. There's more to being a good person than just having a stereo television. You can do it just the way you are!
Vulcan Raven suddenly bringing up the Eskimo-Indian Olympics during his pre-fight taunts, with Snake sarcastically quipping that he must be really good at the muktuk eating contest. Raven confirms this with the same gravity he uses in the rest of the conversation. You are now picturing Vulcan Raven at the Eskimo equivalent of a pie-eating contest (except you are eating a raw slab of whale skin and blubber). TTS changed Snake's quip into a belief that Raven excelled at the "Stick Pull" and "Four Man Carry" events.
After escaping the gas room, and before confronting Liquid at the Metal Gear Rex (before the cutscene starts), get out your sniper rifle and shoot at Liquid's head. Liquid responds by rubbing his face, as if scratching an itch. Of course, this fits with Liquid's ability to absorb a ridiculous amount of damage. note This only works in the PS1 version. The Twin Snakes has the cutscene begin as soon as Snake escapes the gas room.
Liquid gets few (intentionally) humorous moments, but this one referring to his ally Sergei Gurlukovich is pretty amusing. He just sounds so disdainful.
Liquid: Their Regular Army is in shambles, and they think they can restore their country's military power with nuclear weapons?! That Gurlukovich, he's no warrior! He's...he's a politician!
Liquid: Ocelot, you did it again! Ocelot: ...Sorry, boss.
The way Liquid sounds like a disappointed parent is what really sells it.
The sequence in the Otacon ending of the Twin Snakes version, where Snake and Otacon are walking down the snowy pathway. Otacon slips and tumbles down the rest of the way. Snake can only shake his head. Naomi's straight-laced closing narration playing over this just makes it more hilarious.
.Ocelot: YOU IDIOT!