First, when re-infiltrating Shadow Moses Island, Otacon calls Snake to tell him to put in Disc 2, before realizing they were on a BluRay disc, which is dual-layered. Snake tolerates it for all of 3 seconds before telling Otacon to get a grip.
And during the final act, after defeating Screaming Mantis, the ghost of Psycho Mantis shows up to pull his old tricks. But after finding out the system doesn't have a memory card and (if you aren't using the Dual Shock 3) the controller doesn't vibrate, he freaks out and is banished by The Sorrow. Also, the flashbacks that normally call back to images of past games are of a PS1.
His gleeful response to causing the DS3 controller to vibrate is even funnier.
A third callback and funny moment is when you call Campbell for help when dealing with Screaming Beauty. Campbell tells Snake to attack the bust, but as Snake puts it, "There's no bust!"
Metal Gear Solid 4: Snake's Quest for a Good Smoke:
The mission briefing where Sunny just walks up, snatches the cigarette out of Snake's hand, and yells "This is a no smoking flight!". His Psyche meter drains a quarter, like "I just got my ass handed to me by a little girl. I am not a man."
At the end of the Act 5 mission briefing, Snake raises his hand and wiggles his fingers like an eager student. It's hilarious. And then when Mei Ling calls on him, he asks, "Anybody got a smoke?" Meryl groans, and his Psyche Meter drains.
Sneaking up on a soldier and holding them up at gunpoint, patting them down, followed by a very special knockout move. Their high pitched squeal of pain just makes it better.
Even funnier when done on a woman.
All of Akiba's scenes before he took a level in badass.
There's a Codec conversation with Roy and Rose about how Rose is a Lethal Chef. She also states that she likes American military rations, after Roy had said how an international meet he went to found America has the crappiest tasting rations in the world.
Roy:(dryly) America for the win.
Also during that conversation;
Roy: I want you to hear this too. Rosemary: I've heard this a hundred times— Roy: You'll survive.
In what is otherwise a fairly serious scene full of carnage, Ocelot is doing this◊.
While making machine gun noises from his mouth like a five-year-old, one might add.
Should players last long enough against the human forms of the B&B Corps, the mission travels to a white void where not only can you get them to pose for your camera, but playing a particular J-Pop song on Snake's iPod causes them to begin dancing. Looking at the pause menu shows a security cam feed of Sunny doing the dance as well.
A comment on that YouTube link sums this page up nicely - "Solid Snake is the shit, Johnny Sasaki needs to shit, the Patriots are full of shit, and Ocelot is doing stuff justs for shits-n-giggles."
Just before you first encounter the Scarabs, right in the middle of a cutscene, holding down L1 lets you see a bunch of Scarabs pretending to be one guy in a trench coat and fedora. The sheer WTF factor of it is incredible. Best of all, they don't walk—they strut.
During the final battle between Snake and Ocelot, if you allow Ocelot to choke hold Snake and do nothing, Ocelot will kiss Snake on the cheek! Bonus points for the Achievement Trophy for unlocking this is You're pretty good.
Calling up Otacon in Act 1 while hiding in a trash bin gets a conversation where Snake discusses the insects crawling about him (On his face no less) with all the casual indifference of a guy talking about the weather ("I'd hide inside of a toilet if it would help me stay out of sight.") while Otacon is understandably grossed out and demands that Snake wash the smell off of him before coming back.
Early in Act 1, Snake can take advantage of his camo to disguise himself as a statue....grabbing another statue's genitals. Hide with the statue 3 times and Snake snaps the genitals off accidentally.
While meant to indicate that Snake isn't at his best, his Psyche meter dropping by a quarter in cutscenes quickly becomes a Running Gag, and reaches its apex in the The Stinger when it falls as he's faced with the prospect of eating the eggs cooked by Sunny.