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.
Another piece, "Snake Shake", ended up being cut from the ending, but it's still catchy as hell.
"Funny Aneurysm" Moment / Harsher in Hindsight: Snake lands his glider on one of the Twin Towers of the World Trade Center. It'll still be there in 1997, but the plot also features terrorists hijacking a jet airliner and then suicidally crashing it into a New York skyscraper in order to protest U.S. foreign policies. Ouch.
For a brief moment, it actually looks like the hijacked airplane is flying toward the World Trade Center.
Upon further review, it is worth pointing out that in the original Snake was more of an opportunistic Anti-Hero with hints of a Jerk with a Heart of Gold; dangerous and resourceful, but not so ridiculously Bad Ass as the sequel made him.
That said, everybody inside New York has heard of him and heard rumours of his death. Considering that nobody ever comes out of there and that the only news updates that anybody would get is from new prisoners, Snake must have been involved in something major (possibly the Noodle Incident in Kansas City where Brain abandoned him) to have people know who he is.
Particularly notable is the computer image of New York, which is actually a practical effect. What you're seeing is a model of the city with a grid pattern of reflective tape.
The Woobie: Snake. Not so apparent in the movie, but I dare you to read through the Novelization and not see him as one.
Jerkass Woobie: Even in the movie, Snake is not really someone who you would call a Knight in Sour Armor. But let's take a look to his background: he gets betrayed by the same goverments he believed in during the "Leningrad Ruse" (where he lost the use of his left eye) and then all his country is turned into a totalitarian police state, with his parents being murdered by the police in the process. Wouldn't you be a bit sociopathic after that? He does, however, hold a loose code of honor and humanity and he can also occasionally step in the Jerk with a Heart of Gold territory.