Flash Cartridges

You just plug in your E/EEPROM/Flash/NVRAM chip to the socket. You can program this with the arduino, but you will need the datasheet for the chip you're trying to program. It will have timing requirements for program pins and such. Just write your subroutines to program the chip in spec with the timing constraints.

Then you will need a hex editor that will parse your gameboy program into hex values separated by 0xXX, 0xXX, ......
Then in your Arduino sketch, you make an array unsigned of unsigned char, with its size being the size of your hex file.

Then copy the parsed values into the initializer for that array. You will need a for loop to call the programming timing subroutines and increment the address lines and put the hex file data on the data bus.

If you're using an Uno, you won't quite be able to put 32K of gameboy program on it, as the uno only has 32K of flash.

The cart itself is just the gameboy pins connected to the memory chip socket, from what it sounds like on the website.
 
For gba roms on my GBA SP, i got the ez flash iv from 3dstemp. it's said to be compatible with gba/gba sp/nds consoles, and price is cheap. Don't know if this is the one you are looking for.
http://www.3dstemp.com/
 
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