Hyper Ball

Spider Ball

There are only three spots in the game where spider ball is typically required, one of which is to get Hazard Shield, so as long as you are skipping Hazard Shield, you only have to worry about two rooms.

Defense Access

Get out of bounds in Defense Access using Secret World 17, discovered by paraxade.

Mine Lift

Mine Lift must normally be traversed to get Nova Beam. However, it can be skipped by wallcrawling past it with getting out of bounds in Phazon Quarry via Secret World 16, discovered by paraxade.

Hazard Shield

Hazard Shield is the easiest upgrade to skip in Metroid Prime 3, especially if you have several energy tanks in a any%/100% speed run. It is fastest to skip hazard shield in any%, and fastest to get hazard shield after nova beam in 100%.

Note that if you are either skipping spider ball, and/or using the Nova Beam wallcrawl, then you don't need to worry about Mine Lift and Phazon Harvesting, as they are skipped.

Note: After defeating Omega Ridley, the game gives you the hazard shield automatically as it is tied to Samus's appearance. This is likely because there is no model of Samus's suit that is 75% corrupted without the hazard shield.

Command Courtyard

When you enter this room, the far back-right corner has a safe spot from the acid rain, just on the other side of the grapple voltage switch. Screw attack there (you don't take damage while screw attacking), get in the safe spot, and face the grapple voltage terminal. Inch forward very slowly until you can lock on it, then activate it; if you start taking damage from the rain, you moved too far forward.

Skyway Access

When you enter, hug the left wall and move forward until you activate the lasers, then move back. You shouldn't touch the acid rain by doing this. Skip the cutscene (you take damage during cutscenes), and move back before fighting the pirates. Use hyper mode to take them out. There will be another cutscene with four crawltanks; again, skip it as quickly as possible, and move back when you regain control of samus to minimize acid rain damage. Take out all four crawltanks. You will see one more cutscene with the morph ball slot opening on the right wall; skip this cutscene, and go to it as quickly as possible. If you need health, blow up the phazon crates.

Mine Lift

When you enter Mine Lift and tear off the gate via grapple lasso, go to the spider track, using the left spinner first. After activating it, spring ball quickly up to the spider track again and use the other spinner. After activating the second spinner, move down-right to land on a safe spot near the door.

Phazon Harvesting

Skip the first two bridges by screw attacking left just before entering the rain. Get in the safe spot, then use two screw attacks to climb up the bridge that slopes up; there is a safe spot in the back-corner.

Turn left, then climb up the next two ledges; there is another safe spot in the back-right corner. Then either boost ball or screw attack quickly across the last bridge.

Energy Cells

The game intends for you to have five energy cells at minimum to beat the game. However, it is possible to skip having to use energy cells in most rooms in Valhalla. The minimum number of energy cells required to beat the game is one energy cell.

Aurora Chamber

This trick skips having to collect two energy cells. Thus, it is ideal to use this trick as it saves time from having to collect two energy cells in any%; it still saves time even in 100%, as it skips having to put in the energy cells as well as a metroid hatcher fight.

Stand in the center of the room with the data terminal and face the door with the raised bridge. There are some horizontal black bars sticking out from the floor by the door; screw attack into the left edge of the closer bar. If you bonk off the right spot, the game will spawn you just at the door.