Big Lipped Alligator Moment: While Solid Snake is hiding in the sauna, waiting for the brooch to change shape, a naked guard enters the sauna, hangs out a little bit, and then leaves. Granted, the guard is probably there to ensure the player keeps Snake in the sauna the right amount of time, but it's still a pretty random moment.
Even Better Sequel: Or Surprisingly Improved Sequel for those who weren't impressed by Metal Gear. This game features a more complex plot, better graphics, the introduction of the radar, the ability to crawl, enhanced guard AI, and tons of little details. The improvement is so vast that first time players have been stunned by the opening credits sequence.
Harsher in Hindsight: Calling Master Miller during the fight with Big Boss will have him state that Big Boss was a monster. Granted, it's in the context of Big Boss's Super Strength, but this line becomes significantly harsher after Metal Gear Solid: Peace Walker, where he was a former ally of Big Boss and one of the founders of Outer Heaven. Likewise, calling George Kasler during the fight has him mentioning a false rumor that Big Boss has cybernetic limbs to replace the ones he lost during the fight in the previous game. Metal Gear Solid V: The Phantom Pain revealed that he did lose an arm and had it replaced with a mechanical one, long before the events of the first game. Of course, that wasn't actually Big Boss. However, in an almost hilarious turn, the "Big Boss" of the first game, Venom Snake, the Body Double, did have a bionic arm.
A bit of a stretch, but in Metal Gear 2, there were tanks in the hangar (and originally planned to be fought against) that were referred to as Goliaths. The next medium to use the name Goliath in regards to a Main Battle Tank is the TV Drama/TV adaptation Kings.
Big Boss's comment about soldiers being dead weight out of the battlefield becomes somewhat hilarious after watching the Mega 64 trailer of Metal Gear Rising: Revengeance, where Raiden bombed at absolutely every single job his unemployment adviser offered him up until getting a job as a cybernetic private military contractor. It also goes int a bit of Harsher in Hindsight, as the unemployment manager when first meeting Raiden mentions attributes to Raiden's four year unemployment to being the result of an implied terrible economy (at the time the trailer was released, the American economy, not to mention most of the world wide economy, especially the European economy, was undergoing a severe economic crisis).
Gustava's backstory reveals that she fell in love with a Western man named Frank Hunter, whom she intended to elope with. Unfortunately, she was denied U.S. citizenship, and was outcasted as a result. Her death by Metal Gear D hits Snake hard when he reveals that he didn't want to see a woman die in front of him in Metal Gear Solid.
For Gray Fox, he's a Shell-Shocked Veteran who cannot stay away from war as he thought he cannot function outside the battlefield. As the pilot of Metal Gear D, he ended up killing the woman he loved. He thought making a woman happy is something he cannot do. The theme that plays in the conversation between him and Snake is appropriately called "Tears".