Central Intelligence Agency... duh!
But seriously, it means CTR Importable Archive (It's a title you can install(A title can be anything from games, game updates, system update, etc.))
Last edited by pastaconsumer,
, Reason: Update to clarify
"CIA stands for CTR Importable Archive. This format allows the installation titles to the 3DS. CIA files and titles on Nintendo's CDN contain identical data. As a consequence, valid CIA files can be generated from CDN content. This also means CIA files can contain anything that titles on Nintendo's CDN can contain.
Under normal circumstances CIA files are used where downloading a title is impractical or not possible. Such as distributing a Download Play child, or installing forced Gamecard updates. Those CIA(s) are stored by the titles in question, in an auxiliary CFA file.
Development Units, are capable of manually installing CIA files via the Dev Menu."
You can install pretty much anything with a CIA, it doesn't have to be limited to just games. System titles, dlc, patches, dsiware, etc.
They're kind of like those self extracting 7-zips you can download for your PC. They can install stuff to your nand or your sd card.