The Metal Gear series has referenced several other fictional works. This article lists some of these references.
In Metal Gear Solid 3: HD Edition, defeating The Fury will unlock the trophy/achievement "Houston, we HAD a Problem", a reference to the line from film Apollo 13, which was itself based on an accident that occurred on the Apollo 13 two days after its launch.
The achievement/trophy for defeating Steven Armstrong in the DLC storyline Jetstream, "You're Hired!", was a reference to the catchphrase for Reality Show star, businessman, and 45th President of the United States Donald Trump, in the show The Apprentice: "You're fired!" (with the game and DLC at the time being released before Trump announced his plans to run for President). Coincidentally, in the main game itself during the final fight with Armstrong, the latter, while divulging his plans to Raiden, at one point shouts "We're gonna make America great again!". This is similar to Trump's campaign slogan during the 2016 Presidential Election, which happened three years after the game's released. In turn, Trump's slogan was derived from former president Ronald Reagan's campaign slogan when he ran for president against Jimmy Carter.
In the Metal Gear Solid 3: HD Edition, the name of the trophy/achievement "Shagadelic", earned by defeating the Shagohod, is based on the titular character's catchphrase, "Shagadelic, baby!"
The achievement/trophy "Who Ya Gonna Call?" in Metal Gear Solid 2: HD Edition, is a reference to the film's theme song, which is awarded for photographing the ghost in Hold 2, during the Tanker Chapter.
Grand Theft Auto: Vice City
Not in any of the games themselves, but an early trailer for Metal Gear Solid 3: Snake Eater had Naked Snake holding up a GRU soldier and then riding off on what was implied to be the GRU soldier's motorcycle. The GRU soldier then irritably comments that it was a grand theft auto, and then states they were in a jungle, not a "Vice City", an obvious reference to the game series Grand Theft Auto as well as the then-current entry to the franchise Vice City.
In the briefing files for Metal Gear Solid: The Twin Snakes, Solid Snake sarcastically refers to the creation of the Next-Generation Special Forces as a "dinosaur theme park," the setting of the 1990 novel Jurassic Park and its 1993 film adaptation.
The Metal Gear Solid 3: HD Edition has a trophy/achievement that is unlocked after beating The Fear called "If It Bleeds, We Can Kill It." This is a reference of a line Arnold Schwarzenegger says regarding the titular creature.
In Metal Gear Rising: Revengeance, during an optional Codec conversation in Chapter R-05, Courtney Collins attempts to tell the "ketchup joke" from the film before Raiden mentions that he had heard it before.
The logo for the comic franchise Spawn can be seen among crates in the Warehouse section of Big Shell in Metal Gear Solid 2: Sons of Liberty.