Inspired by this video
.5. Screw Attack
A mysterious weapon, as it's unknown what the "energy" it uses actually is. Knowing the Chozo, it could be a supernatural force. Very powerful and allows Samus to float before getting the space jump.4. Omega Cannon
Basically fires nukes with no limit on ammo. The user can even injure themselves. The Alimbic race somehow communicates from beyond their death with a telepathic message, "the Ultimate Power lies within the Alimbic Cluster"3. Zero Laser
Smash Bros Brawl Final Smash. Since it destroys Samus's suit, it probably uses energy tanks as ammo like the Phazon Hyper Mode, but fires them all at once. Was also a very good final smash.2. Sonic Boom
the Annihilator Beam Charge Combo. So powerful that it disrupts time and space, and the visual effect is like shattered glass. Easily the most powerful weapon Samus can get as well.1. Light Suit
Rivaling the Morph Ball in its ability to transform Samus, it literally allows her to travel at lightspeed. It's also the most cryptic suit because it's so late game, you hardly get to use it. For the same reason as in Metroid Trainer's video, it's literally made of the mysterious Light of Aether, which is some kind of supernatural biotic energy. Imagine combining this with Speed Boost!
I'm sure some AM2R upgrade could replace something on this list.
Also, I think my #6 would be the Command Visor that allowed Samus to control her Gunship. Just think of the applications to this in a sequel.