Good ol' IMDB.
After the release of Metal Gear Solid 2: Sons of Liberty (2001) (VG), Hideo Kojima said that he would not direct this game. He wanted a member of his team at Konami to replace him, but none of them wanted to, so he was forced to change his mind and direct after all.
In an interview, Harry Gregson-Williams jokingly said that he might return to compose this game's music "if it's set in the Amazon". At the time, Hideo Kojima actually was planning to set it in the jungle. Gregson-Williams was quite surprised when he learned of the setting.
The codename of the character "Major Tom" is a reference to the 1969 song "Space Oddity" by David Bowie, which is about an astronaut called Major Tom. In the game, Major Tom is even asked "Can you hear me, Major Tom?" This phrase is part of the song's lyrics.
The date of the "Virtuous Mission", 24 August 1964, was Hideo Kojima's first birthday. It was originally 24 August 1963 (his exact birth date), but was moved up a year because he wanted the 22 November 1963 assassination of President John F. Kennedy to factor into the story.
When Snake talks with Director Granin in his office, the theme playing on the radio is the Metal Gear Solid theme. Also, the specifications he shows to Snake are of Metal Gear REX from Metal Gear Solid (1998) (VG). There are also figurines of Metal Gear RAY from Metal Gear Solid 2: Sons of Liberty (2001) (VG) and Jehuty from Zone of the Enders Z.O.E (2001) (VG) visible in the background.
In the mini-game "Snake vs. Monkey", Snake asks Colonel Campbell to ask "Gabe" or "Sam" to carry out his assignment. This is a reference to Gabe Logan, the main character of Syphon Filter (1999) (VG), and Sam Fisher, the main character of Splinter Cell (2002) (VG).
Leave the transmitter in your body for an interesting cutscene behind the waterfall
Johnny Sasaki senior guards your cell.
Ocelot is visible in the final cutscene if you hold R1
The character of Raikov is obviously based on Raiden from MGS2. There are numerous jokes made to the poor American audience reaction and androgenous look and feel of the character.
There are many magazines hidden throughout the game. Most of them are videogame-related but there is a Playboy hidden in the game.
The character of Naked Snake in the game was designed after Sean Connery's portrayal of James Bond. This was done, since in Metal Gear 2: Solid Snake, the character design of Big Boss himself was also originally modeled after the older Sean Connery.
In the timeline at the end of the game, Mr. Sigint joins ARPA, the Advanced Research Project Agency, implying that he is the DARPA chief from the first Metal Gear Solid.
The character design of The Boss was based on actress Charlotte Rampling.
The character of "The End" (as well as the concept of The Boss being Naked Snake's mentor) was based on a scrapped member of Dead Cell from Metal Gear Solid 2: Sons of Liberty called Old Boy (sometimes referred as Oldman). Old Boy (according to the MGS2 gameplan) was a 100-year old former Nazi general who wielded a Panzerfaust as his weapon of choice and was also a mentor to several soldiers, including Big Boss himself. His character was written out of the Metal Gear Solid 2 script because they could not find a way to fit it into the story.