The 3DS uses an SD Card for general storage of additional game data and photos taken with the 3DS.
/DCIM - Photos /Nintendo 3DS - Game Data
Additional game data is stored here:
0000034d - Samurai Warriors Chronicles - USA 0000033b - Ridge Racer 3D - EUR 00000358 - Ridge Racer 3D - USA 0000022d - Face Raiders - EUR 00000227 - Mii Plaza - EUR
All "extra data" under extdata is encrypted. Although these files use 0xFF blocks similar to EEPROM saves, extdata can't be decrypted with the xorpad fail like EEPROM 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>/ 00020500 - Nintendo 3DS Sound 00020400 - Nintendo 3DS Camera
"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.