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.
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.