System Settings allows you to manage various settings, use System Transfer, and use Data Management.
Data Management
3DS
Here you can manage 3DS extra data, and 3DSWare/"Software".
DSiWare
When first using this 3DS creates some management data on SD card. 3DS uses a separate directory than DSi: /Nintendo 3DS/<SomeID>/<SomeID>/Nintendo DSiWare. Filenames are same format as DSi: <titleidlow>.bin. The keys/format for these files are completely different from DSi. A DSiWare export(to SD card) from 3DS is ~0x3bc bytes smaller than an export from DSi.
System Updater
The system updater title is identical to the regular system settings, except only system update is accessible with this.