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 original game also gives us "The Best is Yet to Come", played at both the beginning and end, and Mantis' Hymn, an appropriately awesome theme for one of the best boss fights ever.
In the original, it was a prelude; the Gamecube remake also used it for the battle.
The Menu Music is absolutely great in setting the tone for the game. Unfortunately it isn't available on any soundtrack.
Metal Gear Solid 3: Snake Eater
Snake Eater, the theme song of Metal Gear Solid 3, managing to be both a parody and a spectacular example of 60s spy tunes.
"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.
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.
The Only Thing I Know For Real, Jetstream Sam's theme, describing how the only thing he truly knows is the feeling of killing others, and how he desires a Worthy Opponent who can provide him with a true challenge.
The Stains of Time, Monsoon's Theme, describing how the constant fighting and war has washed away any reasons he had for fighting, until only hate remains.
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.
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.
