There's also the Integral version, which remixes it with some of Solid's sensibilities.
Hell, the entire soundtrack from Metal Gear 2 deserves mention. There is a significant improvement in the quality and complexity of the music, compared to its predecessor - no doubt due in part to the addition of the SCC sound chip, which increased the number of sound channels from 3 to 5.
Encounter. Even though it's a stealth game, it's totally worth getting seen just to hear this.
Metal Gear: Ghost Babel
The final battle against Viper (Ascent) is undoubtedly one of the best boss themes on the GBC.
Metal Gear Solid 2: Sons of Liberty
Notably, this is the first game in the series to bring Hollywood composer Harry Gregson-Williams on board to do the music, and his style shows throughout it and all later Metal Gear games he contributed to.
Let's give MGS2 some love for "Yell Dead Cell". Awesome with an undertone of creepiness that suits the bosses perfectly. Also made it into Smash Bros.
MGS3 Theme. The last part of it plays a remixed version of the second game's ending.
"Way To Fall", the ending theme of MGS3 by Starsailor. Easily up there with several of the Silent Hill themes, if not the most fitting ending theme ever for a game. On a related note: Kojima originally wanted two songs by David Bowie, "Space Oddity" and "Ashes to Ashes", to play during the ending.
Takin' On The Shagohod, the theme of the climactic Shagohod battle. The fight itself is easy, but the music accompanying it is fantastic, conveying that final battle feel perfectly as this is the final fight between you and EVA, and Volgin and what's left of the Shagohod.
The song is repeated when Snake has to crawl through the microwave hallway. And if you can pay attention to the split screen action, it's incredible sadness is made all the more evident as it seems like everyone is failing.
What makes them more awesome is that, like in past games, they play at certain parts in the game; Heaven's Divide is played in the part mentioned above, while Koi no Yokushiryoku is played as Paz's battle theme when she hijacks ZEKE. This is a change from past games, since you are fighting a friend (or at least someone with second thoughts), and not an enemy. What makes it special is that this was what she was supposed to sing during the annual MSF day of peace.
The quiet piano version of Snake Eater also qualifies. It's a good callback to the game of the same name, the part of the game where the flashback scenes tend to take place (it plays "Snake Eater" if you take too long), and in general has sort of a wistful, flashbacky feel to it.
Metal Gear Rising: Revengeance
Worried that Rising won't have awesome music? One of the trailers for the game would you like to know that you're WRONG.
Rules Of Nature is the first song with vocals that you encounter in the game itself. Initially, the instrumental version plays over the Metal Gear RAY fight, until you move to finish the thing off. What follows is a brutalMetal Scream of the song's title that puts emphasis on the ass-kicking that Raiden is putting on the machine. It's especially effective when the boss comes back for more, where it's given a Triumphant Reprise once you take it down for good.
All of the battle themes for the bosses start off as instrumentals in the game, then halfway through the fight they gain vocals and become Image Songs about the characters. And they sure do put the Metal in Metal Gear.
Collective Consciousness, Armstrong's first theme (technically Metal Gear Excelsus' theme), which mixes his desire to rebuild America under his rule, a rule where the strong prosper and the weak are eradicated from this world, with his hate for the established system where everyone is a slave to the status quo, and people fight and die for causes not their own.
It Has To Be This Way, Armstrong's second theme, which now describes how he finds Raiden as a Worthy Opponent, and how he they are both similar in their own ways. Plus points are given to it being a remix of Peace Walker's theme.
The Hot Wind Blowing, what seemed like a wasted song when it was first released on the game's OST turned out to be the theme song for the Blade Wolf DLC-exclusive boss Khamsin, showing off his pride to be a Wind of Destruction and his extreme belief in bringing freedom to oppressed peoples, no matter how much blood and chaos must be shed to do so.
The War Still Rages Within, the end credit theme, reflecting the system that the world is stuck in, and how the only escape is to strike your own way free by fighting for your own ideals.
Metal Gear Solid V: Ground Zeroes
"Here's To You", the Joan Baez version. It serves as a Call Forward to the version in Metal Gear Solid 4, but the instrumentals and tone of the vocals show how different Big Boss and Solid Snake are when nearing the end of their missions. Solid Snake fell into near despair, but never gave up on doing the right thing and accomplished a very bittersweet ending to his mission, freeing the world at the cost of almost everything and only getting a few months to live as shown in the melancholy mood of the song, while Big Boss is in despair as the lyrics of the song allude to but the upbeat tempo reflects how Big Boss justifies everything he does as "right", even if it isn't.
Metal Gear Solid V: The Phantom Pain
From the E3 trailer, Donna Burke's "Sins of the Father". It is all about Big Boss' fall from grace, desire for revenge for what everyone from the world's governments to his former friends to his own mistakes have done to him, and ultimately, his willingness to do anything to strike back and control the world that has hurt him. It is quite the Villain Song, showing how far Big Boss has fallen from the well-meaning but misguided and misinformed person he was in Metal Gear Solid 3, decades ago in his life.