Para-Medic calls Snake "a real Captain Nemo" after he states that his name is John Doe. Akio Ohtsuka, the Japanese voice actor of Snake, had previously voiced Captain Nemo in the anime series, Nadia: The Secret of Blue Water.
Done to Raiden from the previous game. Zero devotes a long radio conversation to the fact that the Raikov mask irritates him, and the mask is used to pose as Major Raikov, the impulsive, despised, and ill-tempered lover of everyone's favorite homicidal lunatic, Colonel Volgin; Snake beats him up and hides him in a locker, with the option of actually killing him. This pleased Raiden's substantial Hatedom to no end. He got better.
In the Secret Theater video Metal Gear Raiden: Snake Eraser, Raiden goes back in time to assassinate Naked Snake/Big Boss and take the role as the main protagonist for himself. He ends up, among other things, getting kicked in the face by Naked Snake during the HALO jump, and is almost raped by Volgin, mistaking Raiden for Raikov.
The Metal Gear Solid 4 trailer also takes a potshot at Raiden, with the crowd booing heavily when he unmasks himself and his getting royally creamed by Snake during their fight for the main character chair.
Doing It for the Art: As detailed below, Akio Ohtsuka was so ready to do all of Snake's dialogue in Russian that he took up language classes for it. However, his castmates found the idea crazy and it was dropped altogether.
Enforced Method Acting: During the scene where Snake and EVA where hiding in a mountain bolthole, when EVA leaned in to kiss Snake, he pulled back. This was because Snake's motion capture actor for the scene wasn't used to doing love scenes and pulled back because he was nervous. Kojima, believing this was in character for Snake, decided to keep the scene in, and fondly remembers this as one of his favorite touches in the game.
The river you "fight" The Sorrow in is often called the "River of Sorrow" by fans, for obvious reasons.
The infamously long ladder climb after the fight with The End is jokingly referred to as the "Ladder Boss".
I Knew It: Why would a hero whose motto is "loyalty to the end" betray her country? She says it herself near the beginning: "I didn't." That she's a Fake Defector never really crosses Snake's mind, but everyone playing the game expected that to be the case. That it doesn't turn out okay for The Boss in the end... that's the real nasty twist.
Recursive Import: Subverted. Metal Gear Solid: Integral and Metal Gear Solid 2: Substance had English voice acting with subtitles for their Japanese releases. However, the Subsistence edition of this game kept the Japanese voice acting for its native release, but still added all the other extra features from the European version.
Throw It In: Kojima wanted to use a piece of licensed music for the closing credits, and a colleague of his suggested he listen to the band stellastarr*. He misheard this as "Starsailor", and liked the track "Way to Fall", which ended up being used.
So My Kids Can Watch: The Snake vs. Monkey minigame in the game which is based on Ape Escape was partially made so that the developers with young children could share the game they were working on with their kids.
The credits theme was originally planned to be David Bowie's "Space Oddity" and "Ashes to Ashes" when space development was originally one of the game's main themes.
As the player goes through the game, Snake's injuries were supposed to leave visible scars on him, but the PlayStation 2's hardware capabilities were unable to handle this feature.
During the torture sequence, there was going to be various button prompts that would have Snake struggle and swear, but the concept was ultimately cut.
Kojima and Akio Ohtsuka proposed the idea of having the game be voiced in Russian. By the Japanese voice cast. Ohtsuka was so enthusiastic about the idea, he went for Russian lessons. The rest of the cast shot them down. Interestingly, he decided to revisit this idea and use actual Russian in Metal Gear Solid V: The Phantom Pain.
The Naked Sample tech demo for the 3DS showcased some significantly improved graphics, an updated sneaking suit design, and new set-pieces showing off the 3D capabilities of the 3DS hardware. Unfortunately, the actual Snake Eater 3D is more of a straight port with updated textures and added game mechanics from Metal Gear Solid 4 and Peace Walker.
The game was originally meant to be a PlayStation 3 title, but it was released for the PS2 instead when the former's development took longer than expected.
The "Guy Savage" nightmare what Snake has was originally meant to be Gradius, but Kojima thought that an original game was better suited for that part.
It was originally intended that Colonel Volgin actually murdered his father which resulted in his inheriting the Philosophers' Legacy by consequence (thus making him a Self-Made Orphan). However, the still that had him murdering his father was cut from the final version. Had it been kept, it should be noted that his reasons for murdering his dad most likely had nothing to do with the Legacy, as he himself admitted that he didn't even know about the Legacy's existence, or even that his father had it, until after his father's demise.
Early press releases stated that the player would be able to set traps for enemy soldiers, similar to the traps that the player must negotiate in the game. Also, there wouldn't be prescribed paths through the jungle, allowing for more freedom in navigation. These features were cut when the PS2 was found to be unable to process these.