MGS2 was almost not released Stateside after 9/11, due to its inclusion of terrorists and its New York setting. A scene depicting the destruction of the Statue of Liberty and much of Lower Manhattan (including the World Trade center Towers) by Arsenal Gear was removed from the game.
The ability to throw grenades round corners and centre the screen via the Options menu were not in the Trial Version of the game distributed with Zone of the Enders. They were only added after some feedback from the game's English and Japanese Bulletin Board Systems reached the development team. These BBSes were overseen by an un-named bilingual KCEJ West employee and monitored by senior development staff, but have since been deleted.
When Raiden meets up with Snake inside Arsenal Gear (before the battle with the Tengu Commandos), Snake tells Raiden he will provide him with ammo if he should run out. Raiden asks Snake how he will do this, and Snake points to his bandana and says "Infinite ammo". This is a reference to Metal Gear Solid, where if the game is completed once by saving Meryl, the player will be provided with a bandana that gives Snake infinite ammo when equipped as an item during the next playthrough. Snake's Infinite Ammo bandana is also included in the Tanker Chapter as an unlockable after acquiring enough dog tags.
Snake adopts the alias Iroquois Pliskin in order to conceal his true identity (as Solidus is posing as Solid Snake at this time). The name "Pliskin" is a reference to Snake Plissken, the main character of Escape from New York and Escape from L.A., who Snake himself is based on and bears a resemblance to in the game (as does Big Boss, mainly due to the eyepatch).
Some of the characters are named after the cards it takes to get a straight in a game of poker, with Solidus being the "King", Fortune being the "Queen", Raiden being the "Jack" and SEAL Team 10 being a reference to the number of spot cards. Pliskin, who is actually Snake posing as a SEAL Team 10 member, could be considered the "ace in the hole" (as he was referred to in Metal Gear Solid).
Stealth and the infinite ammo bandanna can be obtained for the Tanker Chapter after collecting a certain amount of dog tags, whereas in the Plant Chapter, the player receives Stealth, Infinite Ammo Wig, Infinite Grip Wig, and Infinite Breath Wig.
When Raiden acquires the sword in the Plant episode, he can switch over to the blunt side and knock out Snake. When he is out, the player may pick him up and drop him, and will be rewarded with a Dog Tag (though Snake will clobber Raiden when he recovers). Depending on the level of game play, the dog tag will read either Iroquois Pliskin, Meryl Silverburgh, Solid Snake, Liquid Snake or Hideo Kojima.
If, when at the beginning of the Plant Chapter where one must enter their date of birth, you enter the current date, the game will wish you a happy birthday.
Stillman, the bomb defusal specialist in the game, refers to the theme of the game that you must pass more on than just skill. He is talking about how when he was training Fatman, a bombing antagonist in the game, he should have also tought him compassion as well as bomb skills. The theme of the game revealed near the end that "... you must pass more on than genes...pass on your memories and values..." refers to this.
In the game, Raiden states that he's been in over 300 missions in VR training, which is the exact same number of missions playable in Metal Gear Solid: VR Missions. When talking to Pliskin, Raiden in fact quotes the names of modes available in the game, and videos of the game are shown.
In the Tanker Chapter, when Snake is uploading the photos to Otacon, the sequence is accompanied by an amusing digital version of Otacon. It also makes a cameo at the end of the first trailer for Metal Gear Solid 4: Guns of the Patriots, and Kojima recently released a downloadable version of it under the name "OtaClock". It includes a clock similar to the Desktop clock, although more detailed, and also comes with an alarm.
The opening scene for the Tanker chapter

lol you gave me a 10 on interactivity and humor. lol. Well, anyways, I guess the thing about it is the plot really isn't laid down in this animation, it's just supposed to build a mood i guess, ya know?