Brinstar - Metroid (NES, GBA)
I don't know if it was a deliberate decision to give the opening area of Metroid, Brinstar, a triumphant, upbeat theme, but I think it works well. The areas that you'll later transverse in Metroid can become quite difficult and complex so it helps to welcome players with a more lively piece of music.
Kraid's Lair - Metroid (NES, GBA)
While Brinstar, the starting theme of Metroid filled you with a sense of excitement and exploration, Kraid fills you with dread. Despite the limitations of the NES hardware, Kraid's theme is no less a haunting piece of music. It's been remixed quite a few times and the arranged versions are fantastic but I can never get enough of the original.
SR388 - Metroid II: Return of Samus (GB)
Think Metroid: Other M is the black sheep of the Metroid series? You probably haven't played or read about Metroid II. Playing on the Game Boy's monochrome screen Samus' second quest sent her to the Metroid's home planet SR388 where her goal was to exterminate each and every Metroid she encountered. Much of Metroid II's music wasn't anything to write home about. In fact, much of it is uninspired bleeps and blops. But a few pieces do stand out, like the opening SR388 theme.
Brinstar Red Soil Swampy Area - Super Metroid (SNES)
Ask any Metroid fan what their favorite game in the series is and most of them will say Super Metroid. This game was one of the best games to come out of the 16-bit era, blending action, platforming, exploration and even a little horror into the mix. The SNES's enhanced audio power meant that the Metroid music could be fleshed out further. Rather than rely on old themes, Super Metroid uses mostly new music. In fact, the only tune to get arranged is the classic title them from the original Metroid. The Red Soil Swampy Area of Brinstar acts as Brinstar's second section and is also where Kraid is hiding out.
Big Boss Confrontation 2 - Super Metroid (SNES)
The last time you saw Kraid in the original Metroid he was no larger than Samus. When you see him again, he's still about the same height and he's quickly disposed off with some Missiles, even faster if you use a Super Missile. But it turns out the Mini Kraid you killed wasn't Kraid at all. Walk into the next room and you see half of Kraid. Yes, half of Kraid. He's so huge in this game that a single screen cannot contain him. After taking enough damage he'll erupt from the ground to show you his full size. Big Boss Confrontation 2 is right.
Planet Zebes - Super Smash Bros. (N64)
The N64 wasn't know for having a great library of fighting games, but with Super Smash Bros., you really didn't need much else. It was the first game that let Mario, Link, Samus and Captain Falcon beat the crap out of each other for reasons I still don't know. Planet Zebes is a remix of the Brinstar theme from the original Metroid.
Parasite Queen - Metroid Prime (GCN)
I can clearly remember the time before Metroid Prime released. Gamers and critics alike were highly skeptical that a Metroid title could be done in 3D. The last Metroid title was Super Metroid in 1994 and Prime released in 2002, making it eight years since the last Metroid game. Despite all the fears and doubts, when Metroid Prime released, the game was mind-blowing, forcing many naysayers to eat crow. It may have mostly played from a first person perspective but the exploration elements were still there, dubbing Metroid Prime a first person adventure title. This is the game that put Retro Studios on the map and they've been one of the go-to companies for Nintendo when it comes to reviving long dormant franchises.
VS. Serris, Yakuza - Metroid Fusion (GBA)
As if a grand 3D Metroid game wasn't enough for gamers, Nintendo released Metroid Fusion, a 2D adventure, the same day as Metroid Prime. That was $80 on games gone in one day! Fusion tends to hold the gamers hand more than any other Metroid game so the player is never really lost. This was a sore point for a lot of players but it didn't really impact Fusion to the point of it being unenjoyable. On the contrary, Fusion was a marvelous 2D complimentary game to the 3D exploits of Metroid Prime. Fusion had far more bosses then it's predecessor, Super Metroid, some of which could make the player wanna chuck their GBA at a wall. This theme was saved for the more annoying bosses.
Multiplayer Theme 1 (Hunters Brinstar Jungle Floor) - Metroid Prime 2: Echoes (GCN)
After successfully launching Metroid into the third dimension, Retro Studios followed up Metroid Prime with Metroid Prime 2: Echoes. It may not have had the same impact as the original, but it was still a worthy follow up. Echoes brought some multiplayer elements to the table where four players could hunt each other down via split screen. One of the themes used in multiplayer was a kickin' remix of Super Metroid's first Brinstar theme, which was also added to Super Smash Bros. Brawl's extensive selection of music.
Vs. Ridley - Super Smash Bros. Brawl (Wii)
Samus and Ridley seem destined to clash again and again so it wouldn't feel right to not include some form of Ridley's boss theme. In actuality, this boss theme comes from Super Metroid, the Big Boss Confrontation theme. It's heard the first time the player encounters Ridley in the space station at the start of the game. Ridley may not be the final boss of each Metroid title, but he is still Samus' arch nemesis, even moreso than big bad Mother Brain.