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 like "oh shit" before picking it back up.
Even funnier when you remember that in both MGS2 and MGS3 he was spinning a gun around with his left hand in most of his appearances, so this was a legit clumsy moment from Ocelot.
In the PS1 version, when Snake sees Liquid walking towards him and Meryl while they're trapped under the Jeep, and just mutters "Uh-oh", as if this isn't the very worst thing that could possibly happen.
From the Gamecube version, the long pause between Snake's "on the battlefield, you never think about what's next" line and the scene fading out. You can literally feel him regretting saying that.
This gem just before Snake's fight with the Cyborg Ninja:
If you call Miller while on a noisy floor, he'll give the player advice for sneaking around in real life. Snake then remarks, flustered, that he literally can't do what Miller advised.
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." 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.
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. TTS changed Snake's quip into a belief that Raven excelled at the "Stick Pull" and "Four Man Carry" events.
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 and he turns to the grunt who backs off fearfully...before Snake drops like a ton of rocks.
In one of TSS' 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".