Was traversing the web and stumbled across this thread, apparently written a long time ago, but intriguing.
Would his idea be possible?
http://forumsx.sonic-cult.org/lofiversion/index.php/t1237603.html
"In concept, that's a good idea, however the program was made for the Gameboy version of Metroid, and injected the palettes into a location in the rom that was convienent for that game. This, however, usually ended up replacing important data in any other rom, resulting in either messed up graphics or simply causing the game to not run.
Now, I may sound stupid because I know next to nothing about Gameboy Color palettes, but wouldn't it be possible to overdump a rom and use the excess space to store the GBC palettes?"