Libretro with Handy core is another good one (probably the best from the point of view of a gamer, maybe not for a developer, don't know much about the handy version used) but has a bug with eeprom handling. Opened an issue on github proposing a solution, but no one tryed to fix the problem so far.
I though this was merged already w/o my intervention... let me check
all i want to menation is that all that has been done long time ago. it is quite easy. you just have to switch the title pic and first binary address from tghe hardcoded one in the loader to the one which is read from the directory.