The 9.3.0-21 system update was released on December 8, 2014.

Change-log

Official change-log:

Changes to the HOME Menu:

A Shuffle Favorites feature has been added under Change Theme in HOME Menu Settings. Users can choose multiple themes and have their theme change when the system is left in Sleep Mode from the HOME Menu or turned on after being off
Available software updates can now be downloaded from the HOME Menu
Users can now capture screenshots with both the upper and lower screens included

Improvements to system stability and usability:

Further improvements to overall system stability and other minor adjustments have been made to enhance the user experience

JPN New3DS change log:

The following is from Google-translate:

Add "amiibo Settings"
I have to add an entry for the "amiibo Settings" to "HOME menu settings".
You can register the owner and the nickname of amiibo, you will be able to or erase the data written to the amiibo.
Nintendo 3DS software corresponding to amiibo is expected to release in the future.

System Titles

The following new titles were added: Fangate_updater, Old3DS NFC system-module, and the amiibo Settings system-applet.

The following applications were updated: eShop and Nintendo Network ID Settings.

The JPN placeholder New3DS "menu" application was updated, this is still stubbed. Likewise for the USA placeholder "friend" application.

The following applets were updated: Home Menu, Miiverse, memolib, appletEd, PNOTE_AP, and mint.

The New3DS Internet Browser was updated for all regions.

CVer, NVer, and New3DS NVer were updated. The bad-word list and the NZone hotspot list were updated.

0004009B00012302 + equivalent titleIDs for other regions and 0004001B00018002 were updated.

The following system-modules were updated: Cfg, HID, AC, NIM, IR, RO, NS, act, camera(Old3DS), GSP(Old3DS), and i2c(Old3DS).

The following New3DS system-modules were updated: camera, GSP, i2c, nfc, and qtm.

Old3DS and New3DS NATIVE_FIRM were updated.

Multiple system flaws were fixed, this includes a system flaw used in Ninjhax. Ninjhax was not completely blocked.

Support for amiibo was added. Support for the Old3DS NFC peripheral(which communicates with 3DS via IR) was added.

Various(perhaps all?) updated(minus the application stubs) New3DS titles now use New3DS-specific NCCH crypto, see here.