On the 3DS savegames are stored much like on the DS, that is on an EEPROM in the gamecart. On the DS these savegames were stored in plaintext but on the 3DS a layer of encryption was added. This is highly likely a streamcipher, as the contents of several savegames exhibit the odd behaviour that xor-ing certain parts of the savegame together will result in the plaintext appearing.
So how do you use this to decrypt a savegame on a 3DS? First off, you chunk up the savegame into 512 byte chunks. Then, you bin these chunks by their contents, discarding any that contain only FF. Now look for the most common chunk. This is your keystream. Now XOR the keystream with your original savegame and you should have a fully decrypted savegame. XOR with the keystream again to produce an encrypted savegame.
Savefiles stored on the EEPROM are using a custom FS.