SD Filesystem

The 3DS uses an SD Card for general storage of additional game data, music and photos taken with the 3DS.

/DCIM - Photos and images downloaded with the Internet Browser
/Music - Music Files
/Nintendo 3DS - Game Data

Additional game data is stored here:

/Nintendo 3DS/<SomeID>/<SomeID>/extdata/00000000

0000008f - Some 2.0.0-2 data, unknown doesn't appear in extdata management.
00000207 - Mii Maker - JPN 
0000020d - Face Raiders - JPN
00000210 - Some 2.0.0-2 data, unknown doesn't appear in extdata management.
00000217 - Mii Maker - USA
00000219 - eShop 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.

With the introduction of the June update the folder structure changed slightly. You will now find "dbs" and "title" folders located in /Nintendo 3DS/<SomeID>/<SomeID>/ along with the extdata folder. "dbs" contains two files, import.db and title.db - usage currently unknown.

/title/00040000/ appears to contain eshop downloads (can someone verify these and add for different regions?):
00054e00 - 3D Classics Excitebike - EUR (verified)
00054300 - 3D Classics Excitebike - USA
00032600 - Pokedex 3D - EUR (verified)

"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.