Wall-jumping: The game teaches you this trick, but not its numerous applications. For instance, wall-jumping lets you access all areas in Bubble Mountain starting from the save point door and get Wave Beam without using Grapple Beam. It's also really fun.
Crystal Flash: Get below 50 energy with empty reserve tanks and have at least 10 missiles, 10 super missiles, and 11 power bombs. Lay a power bomb, then hold L, R, down, and shoot. Your health will be fully restored at the cost of all that ammo.
Beam Combos: Equip Charge Beam and only one other beam type, then select power bombs and charge. This will produce one of four beam combos. Pictured is Ice Beam's version; the most practical one is Wave Beam's, since it can be used to greatly damage various bosses, albeit with frustratingly precise timing. (I'm looking at you, Phantoon.)
Infinite Bomb Jump: This, along with Crystal Flash and Beam Combos, is actually shown in Super Metroid's own intro demonstration videos. Simply lay bombs with correct timing to bounce upward forever. The easiest way is to lay them roughly where the higher bomb is in this screenshot.
Bomb Spread: Morph into a ball while your beam is charged. You'll drop five bombs. Not very helpful, but it looks cool.
Save the Animals: Go to Bomb Torizo's room while escaping after killing Mother Brain. Shoot the right wall to make an exit for the Etecoons and the Dachora (not featured--normally it teaches you how to shinespark). Before Zebes explodes, you can see a small light fly away from the planet.
Kraid Quick Kill: Shoot a charged shot at Kraid's eye while his hand is low to freeze it in place. When his mouth opens precisely this much, shoot it with a super missile, freezing it as well. Quickly hit him with 3 more to kill Kraid before he can even stand up.
Mockball: Maintain running speed as a ball. Run and jump, press down just as you touch the ground, then hold right/left (the same direction you jumped). This lets you pass through this room without Speed Booster and get super missiles before Spore Spawn.
Speedball: Simply a mockball with Speed Booster properties. Breaks all the same block types as regular blue-coloured Samus.
Green Gate Glitch: Open a green gate from the wrong side by shooting a super missile at very close range while aiming upward and jumping. For some reason, this only works on gates facing left. Blue gates can also be opened from the wrong side, but that is
Short Charge: This one is complicated. You can stutter-step (tap left or right) before holding the run button to charge a shinespark faster. You can also tap the run button several times when Samus' back leg is in the air before holding it to further decrease the required distance.
Shinespark Tricks: Shinesparking opens up many possibilities. It lets you skip Grapple Beam entirely, since you can shinespark into the Wrecked Ship and to the top right of the Maridia Grapple Beam room. Short charging lets you shinespark to damage Draygon.
I hope you enjoyed my guide :) Feel free to use the donation button at the top, but honestly, that money would probably be better spent on Free the Children or the Humane Society or some other charity.