Super Metroid's title music, probably still the most ominous piece ever used in the series, even after all these years.
In Super Metroid, the "Crateria Theme" makes a dramatic return at a critical point in the final boss battle just after Mother Brain murders the Baby Metroid. There isn't a player alive whose heartbeat, EEG reading and adrenaline release rates didn't all immediately synchronize with the pulsing bass rhythm, prior to blasting the everloving fuck out of Mother Brain with the newly-acquired Hyperbeam whilst screaming the blackest curses in their vocabulary.
Metroid: Zero Mission right after the zero suit sequence. You've been hiding and running from space pirates when suddenly you get your power suit back and it's more powerful than ever. Cue the AWESOME musicthat makes you feel invincible.
Two remixes of Crateria's Caves in Zero Mission for clever purposes. During the "Solid Samus" portion of the plot, an arrangement similar to the Super Metroid version serves as the "!" music, while a sedate version closer to the Corruption version plays after the guards stand down.
Mother Brain's theme song in Super Metroid as she's handing your ass to you on a silver platter. In a game full of brooding slow- to mid-paced tracks, this theme song manages to sound refreshing, if not outright sinister!
Prime took the already cool Lower Norfair and remixed it for Magmoor Caverns and it was promoted to pure Awesome.
Any player who had sat whistling the menu screen music from Metroid Prime was made endlessly happy by the incredible end credits music. And apparently it's in the Dorian scale, too, which makes it all the more awesome.
The theme for Flaahgra was glitched in the first US release for Metroid Prime causing it to repeat the first part throughout the whole battle. It wasn't until the normal English version, the Player's Choice versions and Metroid Prime: Trilogy came out until we got to hear how awesome it really was.
Possibly because it is quite much Beeps and Boops, or because it was the graphically most awesome level (Tetris flood, glowy things and, for once in all those Metroid games taking place on half-abandoned planets, a massive sprawling city), there's few things not to like about Sanctuary Fortress in Metroid Prime 2: Echoes.
Special mention must be made to Gravity, a piece that takes Nightmare's already foreboding theme and makes something truly nightmarish out of it.
Viewers of ScrewAttack's "Top 10" videos probably recognize the tune in the background at the beginning and towards the end as a Metroid remix, and may be wondering where to find it. Well, look no further!