Ah, good old Pogoshell and the GB Bridge. There's actually something called
Pogobridge, released by Newbie that was an interesting take on the idea of merging Pogoshell and GB Bridge in a less-hacky way. Much, much later, I ended up merging the functionality into my fork of
Pogoshell v2.0b3. I tried to make the process as pain-free as possible, although I'll admit that my documentation is probably lacking since there's a lot to it all. :/ Also, I made a hack of
GBC2GBA, the GBC loader used with the GB Bridge, to have more color control as well as tweak the above mentioned glitchy colors (it happens with SML too, IIRC); I have no idea on the cause, btw. I also really considered trying to import the whole GBC bios palette loading thing into GBC2GBA (as the GB Bridge appears to the GBC/GBA as a GBC and hence the GBC bios can't load a game's palette), but that's a good bit of hassle I haven't gotten around to doing.
In any case, if you are interested in going that route and have problems with the otherwise rather bare details, please let me know.