These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
"Funny Aneurysm" Moment: Near the beginning of Raiden's section, the Colonel talks about how oil leaking out of the Big Shell would be the worst ecological disaster in history, killing all the marine life and ruining the coastline for generations. After the BP Oil Spill in the Gulf, a bit of oil leaking out of the Big Shell (as opposed to rushing up from the sea floor) doesn't seem quite so bad in retrospect.
Similarly, the reason why Raiden was designed as a bishonen character is because a particular fan-letter from a fangirl stated that she didn't want to play as "an old man". Come Metal Gear Solid 4: Guns of the Patriots...
Substance has Raiden wearing Gray Fox's Cyborg Ninja outfit for VR missions. It seems fun now, right? Well, it won't be fun or amusing after playing Metal Gear Solid 4: Guns Of The Patriots where Raiden does become an actual Cyborg Ninja under painful and extremely tragic circumstances.
Game Breaker: The stinger missiles Snake gives Raiden make the boss fight against Vamp a piece of cake.
The M9 tranquilizer handgun, or the silenced SOCOM. Take your pick. Both are capable of instantly incapacitating headshots from distances that only a Sniper Rifle would remain accurate at in Real Life, the ammo is extremely common, and abusing them almost guarantees you never being seen. The M9 is arguably the better of the two since you don't aim it down the iron sights, meaning the gun takes up less of the screen in first-person view, and the laser is much easier to line up shots with than the SOCOM. Plus, your endgame status is better if you don't kill anyone. Extra points since it's a Disc One Nuke. The silencer for the SOCOM comes literally about an hour into the game later though.
Long-range sniping using a scope and a pistol is possible in this game, as well as in Snake Eater, via a complex sequence of button presses. Go to first-person mode, zoom in, switch weapons while still holding the first-person button, hold the fire button to aim and then immediately let go of the first-person button. Wherever you were looking at in first-person, your weapon will be aimed directly at it, no matter how far you zoomed in.
Harsher in Hindsight: Snake's warnings about the dangers of "turning war into a video game" can seem even more chilling today that they did in 2002, now that military-themed first person shooters (often praised/criticized for their unprecedented realism) dominate the video game industry, and facing off against real people in virtual death matches has grown into a common hobby.
Alternatively, an I Knew It on the part of the game.
The issue of censorship and intel concerning the Patriots, then the PATRIOT Act of 2001, effective 2002. Possibly an I Knew It on the part of the game as well.
Hilarious in Hindsight: The premise of the game being a computer program with implied sentience manipulating all of humanity and causing a lot of atrocious deaths via a terrorist group all for an "experiment," and that program being voiced by Paul Eiding, gets very interesting when Dirge of Cerberus does something VERY similar for its plot.
Also, Raiden recalling that he never actually met the Colonel even once will sound pretty funny after Metal Gear Solid 3: Snake Eater, where Raiden's expy in that game, Major Ivan Raidenovitch Raikov, definitely knows a colonel.
The cardboard box is labelled "The Orange". Get it?
Inferred Holocaust: Thanks to various cuts within the final version due to the unfortunate timing of its release, Arsenal Gear crashing into Manhattan as well as the results was glossed over.
It Was His Sled: By the time of the release of the PC port of the game (around 2003, two years after the game first came out for the PS2), reviews of the game had already abandoned trying to keep the game's Decoy Protagonist a secret. That, and everyone knows that the game's ending is, err... rather demanding of the player.
Nightmare Fuel: Everything that happens after Emma's death is so fucked up that you cannot tell what is real and what is not anymore. The Fission Mailed screen is particularly disturbing - with the obviously twisted English words and you still fighting alright.
Especially consider the meaning behind the words Fission Mailed, along with "Emit" and "Continent" - all those words carry an ominous meaning toward the villains' next move...
The AI!Colonel's last words to you before you fight Solidus are a hideously rasped and digitally distorted "Our beloved monsters — enjoy yourselves." All the while, it flickers between its recreation of Campbell's face, and a skull, which leers at you.
Older Than They Think: BioShock was acclaimed for its deconstruction of the concept of linearity in video games, but this game beat it to the punch by six years.
Sons of Liberty was not the first game in the series to order the player to shut off their console. That credit goes to the first game in the series.
Porting Disaster: The PC version. You know you've screwed up when you fail at porting a game that worked perfectly fine on the Xbox to PC, when the architecture is nearly identical between platforms. It was so bad, in fact, that no MGS game since then was ported from its original console until the HD Collection in 2011 (a full seven years after MGS3's initial release), and it took another two years for any to come to PC (Metal Gear Rising: Revengeance in January 2014, nearly eleven years after the MGS2 PC port).
Protection from Editors: Might be the reason why the game turned out the way it did. Apparently Kojima's original script was over 800 pages long.
Recycled Script: An Invoked Trope. Metal Gear Solid 2's plotline is almost a clone of Metal Gear Solid's plot, which in itself was recycled from the MSX games (specifically Metal Gear 2: Solid Snake). Unlike Metal Gear Solid, however, the game makes it a point to mention the similarities between the events in it and the events of the previous game, which ultimately ended in a deconstruction of the very concept of sequels having suspiciously similar plots to their predecessors.
Special Effects Failure: During cutscenes, weapons that the player has equipped with a suppressor will still be as loud as if they were unsilenced. Might be Gameplay and Story Segregation combined with an aversion of Hollywood Silencers, except the same happens if the player equips the M9 before entering the cutscene, at which point it will take the place of the SOCOM in cutscenes it's used in, where it will fire semi-automatically (it's slide-locked) as loud as the SOCOM (it has a suppressor from the start) while drawing blood when people are actually hit with it (it's a tranquilizer gun).
Stop Helping Me!: In the Plant mission, your support team can get on your nerves.
That One Level: Arsenal Gear-Jejunum, where you have to sneak past Tengu guards butt-naked (which prevents you from using your chokehold), and if you get spotted, you're pretty much screwed and have to run all the way back to the torture room to get them off your tail.
The Untwist: Iroquois Pliskin is actually Solid Snake. Word has it they made it as blatantly obvious as possible just to see if anyone would fall for it anyway.
Values Dissonance: Part of the reason for Raiden's lukewarm reception in the West. In Japan, there isn't nearly as much stigma against men with feminine features, and it's actually very traditional to cast them in heroic roles.
Values Resonance: One of the villains' main goals is to try to censor the Internet, only making information that fits the party line available to the public. What was essentially an eight-hour commentary on the Japanese textbook controversy has taken on a newlight a decade later. Bear in mind that the game was released in 2001, long before Internet users were considering this a major concern and absolutely online anonymity and freedom were essentially givens.
Vindicated by History: Though its gameplay was generally praised, its story was seen as convoluted. However, as years go by, many are finding it to be an excellent early example of post-modernism in the video game medium, as well as a decent deconstruction of But Thou Must games... two traits that would later be championed by the critically acclaimed BioShock.
Waggle: The pressure-sensitive controls are highly awkward (at first), especially for the assault rifles (even after you're used to them). Lightly pushing the button to shoot will make you aim your weapon, while depressing it fully fires it. This is an important distinction, as accidentally shooting guards you're holding up can be very annoying. In addition, movement with the D-pad is also pressure sensitive—pressing a direction lightly causes the player character to sneak fairly quickly, while a full depression causes you to run noisily. MGS3 fixed this, where normal movement is now solely on the left stick and the D-Pad is for sneaking more sneakily.