I use an ext2 filesystem mounted on /media/mmc2 to store maps on my mmc card.
It's 1KB block size wastes less space than FAT32's 4KB and much less than FAT16's 32KB cluster size (for my 800MB partition).

There's also a 128MB FAAT32 partition (for mmc1) and a 64MB swap partition on my 1GB card.