1) Speed Booster
First Appearance: Super Metroid (1994)
Remember how I said that at face value the Space Jump was the coolest powerup? Well the Speed Booster lets you run really fast and break through things. Exciting, but nothing to write home about. So why in the world is this #1 on my list?
For starters, if you are running and hit an upward slope and jump, you'll keep the momentum and likely somersault all the way across the screen. You can also crouch during the run to store up the power and launch yourself either vertically or horizontally until you hit something that you can't destroy. This technique, known as Shinesparking, allows you access to areas of the game you wouldn't normally be able to get to. You can do this in Morph Ball form in Zero Mission, adding to the functions already neat capabilities.
This sounds pretty cool in itself, but this is used to solve some pretty elaborate puzzles involving maintaining a boost over an extended period of time. One of the most famous comes from Fusion, where it can be used to escape from Sector 4 towards the end of the game. Upon reaching the Navigation Room, instead of the usual dialogue your computer congratulates you on your resourcefulness, and breaks the fourth wall by asking "I wonder how many players will see this message?".
Metroid is filled to the brim with amazing abilities and powerups, but none more so than the Speed Booster.
1) Hyper Beam
Of course it's the hyper beam. You get it for 30 seconds, but it's amazing! It lets you shoot devastating rainbows at Mother Brain! How cool is that. (Spoilers) Plus you get it from her powers after they are sucked out of her by that super sweet Metroid! Who wouldn't love this thing? That's why it's number 1!