I just wanted to let other posters know that I've contacted Spacy51, one of the programmers working on VBA-M, which is basically an on-going work-in-progress dedicated to improving Visualboy Advance and integrating in it all the features from the various ports and versions of VBA.
I asked him about the possibility of including a way to completely remove the background to make it easier when taking screenshots to make maps. We recently determined that the default color that appears when a game doesn't actively displays anything is the first color in the background palette, which can be a problem if that happens to be pure black which is also often used in a game's graphics. Yeah, that infamous problem I've affectionately named "black-on-black removal problem".
Anyway, I don't know if such a feature might be implemented soon, but it didn't seem to be to much of a problem to him, and he mentioned that a hack could be worked out that would replace that background color with pure white (RGB #FFFFFF) which is outside of VBA's palette and thus, never used by a game, but which would only work if the Windows display is set to 24/32 bits color.
Anyway, I'll keep you guys informed of any development on this.
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Current projects: Metal Storm (NES), Clock Tower (SNES), Ristar-The Shooting Star (Gen), Sonic The Hedgehog (Gen), Sonic CD (Sega CD), Mega Man Zero (GBA), Battletoads (NES), Bucky O'Hare (NES)