The Nova Beam, which stacks with the Power and Plasma Beams.
Stacking is a gameplay concept in the Metroid series, which allows Samus Aran to retain the previous effects of any ability and use them in conjunction with the most recently collected upgrade.
Throughout the games, this has applied to numerous upgrades of the Power Suit. The two earliest games, Metroid and Metroid II: Return of Samus had little to no stacking, while Super Metroid was the game that introduced it. It has been present in every game since except Metroid Prime, Metroid Prime 2: Echoes and Metroid Prime Hunters.
Beam upgrades
In Metroid, the Long Beam could be used in conjunction with the Normal, Ice and Wave Beam. However, neither the Normal, Ice, nor Wave Beam could be used simultaneously. This was changed in the remake, Metroid: Zero Mission, which allows Samus to stack her Beams. An unused option in the game would also allow her to enable and disable certain Beams as in Super Metroid. This option was also removed from Metroid Fusion.
As stated, Super Metroid implemented stacking on a higher level. All of the beams could be used simultaneously. However, the Spazer Beam and Plasma Beam were incompatible. Nevertheless, there is a certain glitch that would allow Samus to use both the Spazer and Plasma Beam simultaneously.
Metroid Prime, Echoes and Hunters do not allow for stacking of Beams. Instead, there is a Beam Select option which allows Samus to switch between her Beams to overcome obstacles. Due to the introduction of Hypermode in Metroid Prime 3: Corruption, stacking returned and so the Plasma Beam, when acquired overwrites the Power Beam, and the Nova Beam overwrites the Plasma Beam. With all Beams collected, Samus is able to retain the rapid fire rate of the Power Beam, the burning properties and welding abilities of the Plasma Beam, while also gaining the ability to penetrate Phazite in conjunction with the X-Ray Visor.
While Echoes does not feature stacking in the traditional sense, the Annihilator Beam can be considered a pseudo-stack, in that it requires both the Light and Dark Beam to be used as it uses both of their ammo types. It is capable of opening portals of either polarity, harming creatures of both Aether and Dark Aether, and energizing Light Beacons and Light Crystals. However, it is incapable of opening white or purple hatches.
Like Metroid and Metroid II: Return of Samus, Metroid Prime and Metroid Prime 2: Echoes are the first two of the Metroid Prime trilogy without stacking, and like Super Metroid, Metroid Prime 3: Corruption is the first of the trilogy to introduce stacking beams.
Power Suit upgrades
Samus was also able, in Super Metroid, to use the Varia Suit and Gravity Suit, allowing her to resist heat damage, reduce attack damage, move freely under water, as well as lava. This is retained in Fusion, Zero Mission and Metroid: Other M.
In Metroid Prime, Samus is able to combine her Varia Suit and Gravity Suit, much like she did in Super Metroid. There is also a new type of suit called the Phazon Suit, which protects Samus from blue Phazon. In the end, Samus is resistant to heat damage, can move freely under water, and come in contact with Phazon without taking any damage. The fully upgraded Suit does not protect her from lava or red Phazon damage, however.
Echoes is the first game to make an upgrade obsolete with another upgrade. The Light Suit makes the Dark Suit practically useless further in the game, as it renders the air of Dark Aether entirely harmless. The Dark Suit had previously filtered out 80% of the air's corrosive effects, causing Samus to lose one unit of energy per second when exposed as opposed to five with the Varia Suit. She is never able to protect herself from Phazon during Echoes, however. This forces her to avoid it completely, except during the final battle with Dark Samus.
Missile upgrades
Metroid Fusion is the first Metroid game that allows Samus to stack her Missiles. The Super Missile in this game is an overwrite of the normal Missile, which is then enhanced by the Ice Missile, and finally the Diffusion Missile. In other games, Super Missiles are either a separate upgrade with equal or lower amounts of ammunition, or a Charge Combo of the Power Beam. Corruption adds the Ice Missile effect onto Samus's normal Missiles as well, which can be enhanced with the Seeker Missiles.
Other stacked upgrades
Metroid Prime 3: Corruption introduces grapple stacking. As the game goes on, Samus is able to upgrade her Grapple Beam with a lasso, swing, and the ability to drain or fill objects with energy.