Actress Allusion: Snake and Johnny Sasaki are reminded of Meryl Silverburgh when they see Olga Gurlukovich. There's a good reason for that. In the Japanese version, Meryl and Olga were both voiced by Kyoko Terase.
Approval of God: Though the VR Theory was shot down by Kojima (see below), he included numerous nods to it in Substance, particularly "External Gazer": While testing out Otacon's newest toy, a VR helmet, Snake is tricked into believing he's Raiden and starts to experience bizarre scenarios.
Hey, It's That Guy!: Kelly Brook, Carmen Electra and Louise Rednapp appear in the pin-ups in the initial release of the game. When it was re-released, Konami didn't re-license the images from FHM.
To a lesser extent, most of the game's music was composed by Harry Gregson-Williams (He composed music for Armageddon and The Rock.) Kojima was inspired to have him compose the soundtrack after he and sound director Kazuki Muraoka saw The Replacement Killers in a cinema (Gregson-Williams had composed the music for that film as well) and found they enjoyed his compositions.
Likewise, Naomi of the previous game returns as Emma, and would later share a game with Solidus's voice actor as Bastila Shan.
Olga in the Japanese version is MerylSilverburgh, something that's even lampshaded in the game itself.
Jossed: Give the ambiguity of Raiden's perceptions of realty and the bizarre ending, some fans hold that the entire game is a VR simulation gone berserk; the final pitched battle against the RAY army takes place on a platform which is identical to the one in the VR Missions expansion game. As of Metal Gear Solid 4, this has been Jossed, though it's also been speculated that this interpretation was Kojima's original intention and he merely buckled under fan pressure in between games. *Inception horn*
Meaningful Release Date: At least one trailer pointed out that the game was released during the Chinese Year of the Snake.
Reality Subtext: "[We should] let our children read our sad and messy history by its light," says Solid Snake. While the game was in production, there was a major controversy about the Japanese government whitewashing World War II atrocities in school textbooks.
Talking to Himself: Solidus Snake and Solid Snake are both voiced by Akio Ohtsuka in Japan, and they exchange lines during Raiden's first encounter with Solidus.
Too Soon: The game was released shortly after 9/11, and as such a sequence where Arsenal Gear crashes through Manhattan was severely chopped down. The game jump-cuts from Arsenal Gear accelerating down the Hudson River with the music swelling dramatically, to it having already reached Federal Hall. Though the original version of this sequence is featured in the European Extreme difficulty.
What Could Have Been: The Document of Metal Gear Solid 2 reveals a variety of cut content from the game. For example, Snake was supposed to plant C4s on RAY (similar to his work with Philanthropy), not just take pictures. This sequence made it into Snake Eater during Naked Snake's sabotage of the Shagohod factory.
In addition, the Tanker sequence was intended to end with an escape sequence as Snake tries to make it out of the tanker before it sinks, but the sequence was cut because play testers didn't think it was fun enough(!). Footage of the cut sequence is still used in the main game itself, in flashbacks.
There were supposed to be two additional members of Dead Cell (Old Boy and Chinaman). In Chinaman's case, his boss encounter was in an area that was eventually used for the fight with Vamp.
Raiden was also supposed to unlock a “Mantis Mode” where he can equip Psycho Mantis' gas mask and read the thoughts of NPCs. This sounds suspiciously like it was retooled into the directional microphone.
The scene of Arsenal Gear crashing into Lower Manhattan was cut out of respect for the Sept. 11th attacks: It was planned as a pretty brutal sequence, with Ellis Island and the Statue of Liberty being toppled like bowling pins (you can see why it wouldn't fly, even today). What isn't generally known, though, is that Snake was supposed to join Raiden for the finale, battling Liquid Ocelot and Solidus Snake as a crowd of rooting civilians and mounted policemen look on!