Where are stored the savegames?
Nintendont uses an individual memory card image per game.
To generate and enable memory card emulation, enable "MC Emulation" in Nintendont options and choose the size of the memory card.
The memory card will be created in /saves/<GameID>.raw located on the same partition than your game.
If you enable "multi" as memory card settings in Nintendont options, it will create a single memory card called ninmem.raw which lets you save multiple games on the same memory card file. Attention: do not save Japanese games on the same memory card than non-Japanese games.
The memory card emulation is not 100% stable and your memory card can be corrupted.
If you care about your game progress, always make regular backups of your files!
If you card is corrupted, you can try these links:
http://gbatemp.net/threads/gcn-memcard-recover.349406/
http://gbatemp.net/threads/gamecube-memory-card-corrupt.367902/