Metroid Zero Mission: All Tilesets

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[EDIT] Metroid Fusion tiles are gonna take way longer since the tiles contain absolute black, and the background in the tile viewer is absolute black, too. I'll have to grab them the old-fashion way.

If you're using the VBA tile viewer, you can change the alpha colour with cheatcodes / ram edits.
Hang on, we had a topic somewhere.

Ah, here!
Mainly this post (ram edit) or this one (cheat codes).
They should affect the tiles in the tile viewer, too!

If you're using a stand-alone tile viewer like TiledGGD, you could change the palette data within the ROM, too, but that'd be a tiny bit more tricky. I could probably walk you through it, though.