The 3DS uses an SD Card for general storage of additional game data, music and photos taken with the 3DS.
/DCIM - Photos /Music - Music Files /Nintendo 3DS - Game Data
Additional game data is stored here:
/Nintendo 3DS/<SomeID>/<SomeID>/extdata/00000000
00000207 - Mii Maker - JPN 0000020d - Face Raiders - JPN 00000217 - Mii Maker - USA 0000021d - Face Raiders - USA 00000227 - Mii Maker - EUR 0000022d - Face Raiders - EUR 0000030c - Nintendogs + Cats - EUR 0000032d - Super Street Fighter IV 3D - USA 0000033b - Ridge Racer 3D - EUR 0000033c - Super Street Fighter IV 3D - EUR 0000034d - Samurai Warriors Chronicles - USA 00000358 - Ridge Racer 3D - USA
All "extra data" under extdata is encrypted. Although these files use 0xFF blocks similar to FLASH saves, extdata can't be decrypted with the xorpad fail like FLASH saves. All "extra data" files can't be copied to other 3DS SD cards, they are locked to the console.
"Private" data is stored here:
/Nintendo 3DS/Private/<Title ID Low>/
00020400 - Nintendo 3DS Camera 00020500 - Nintendo 3DS Sound
"Private" data for 3DS Sound/Camera are cleartext.
Under the camera priv dir is phtcache.bin, this seems to list the pictures on SD card?
Under the sound priv dir is: voice/XX/*.m4a. Where XX is 01-10, with sound saved as .m4a.