I don't know of any, and it's been slowing me down while mapping Clock Tower.
Snes9X and ZSnes are both still in development I believe; while the frame advance thing might be harder to include, changing the "empty" color should be easy. You might try suggesting it in their respective forum, and they just might include it in a future version.
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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)