Super Missiles are powerful, more concussive upgrades to the Missile throughout the Metroid series. They are bulkier in appearance and are green tipped, as opposed to slim, red-tipped Missiles. They are used to destroy certain armor and enemies, as well as clear away extremely dense materials such as Cordite.
Metroid Zero Mission
In Zero Mission, Super Missiles worked similar to the way they did in Super Metroid, being a separate weapon acting as a more powerful alternative to regular missiles. They are not required to beat the game using secret passages, and there are various ways of obtaining the Super Missiles, as any Super Missile Expansion will award Samus the Super Missiles. They are a reward for defeating Kiru Giru and Samus can't leave the room without using the Super Missiles.
The Super Missiles first surfaced in Super Metroid, where they are as powerful as five ordinary missiles. They are also used to open green doors. The impact of one of these missiles will cause the screen to shake and will dislodge any nearby enemies which happen to be crawling on the walls and ceilings.
In Metroid Prime, Super Missiles are the Charge Combo for the Power Beam. They are fired by readying a Charge Beam shot and firing a missile. A Super Missile's firepower is approximately equivalent to five missiles and take up five missiles per use.
The Super Missile upgrade is acquired after activating the Space Pirate's Astronomical Holographic Projector in the Observatory of Phendrana Drifts, lowering the upper node upon which the upgrade rests.
Metroid Prime 2: Echoes
Super Missiles return as a charge combo in Metroid Prime 2: Echoes, functioning nearly identically to the Metroid Prime incarnations. Super Missiles in Echoes have the added capacity to open green doors.
The Super Missiles appear in Metroid Fusion, unlike other incarnations, stack onto the Missiles' power. They replace Samus's regular missiles and are enforced with Ice capabilities when Samus obtains the Ice Missiles. After obtaining the Super Missile upgrade from a Data Room in Sector 3 (PYR), Security Robot B.O.X. attacks her. She defeats it with her newly acquired upgrade.
Samus firing the Super Missile after acquisition in Metroid Prime 2: Echoes
The SA-X firing a Super Missile