FBI is an open source CIA (un)installer.
Current Version: 1.3.8
Features
    Available as a CIA, 3DS, and 3DSX.
    Install, uninstall, and launch applications from both the SD card and NAND.
    Delete CIA files from the SD card.
    Install or delete all of the CIA files in a directory at once.
    Install CIA files over the network using sockfile.
    Detailed error output, making it easier to figure out why an (un)installation failed.
sockfile
sockfile is a command line utility (java -jar sockfile.jar <ip> <file>) that can be used to send CIA files over the network to FBI. Press "Y" to display the 3DS's IP address and listen for network installation requests.
Alternatives:
FalconPunch (Python, by mooglazer): 
https://raw.githubusercontent.com/block ... onPunch.pySocketPunch (GUI, by Joshtech): 
http://gbatemp.net/threads/release-sock ... le.386762/Screenshot(s)

    Downloads
    Binaries are typically built from the latest source commit, at the very least being updated after major changes.
    FBI
    Binaries: 
https://github.com/Steveice10/FBI/releases    Source: 
https://github.com/Steveice10/FBI    sockfile
    Binaries: 
https://github.com/Steveice10/sockfile/releases    Source: 
https://github.com/Steveice10/sockfile    FAQ
    Q: Can I install any CIA I want via Ninjhax? / I'm getting an "Invalid signature" error!
    A: No. Without something that patches signature checks, such as emuNAND or a CFW, you cannot install CIAs that are not properly signed.
    Q: I'm getting a "Database does not exist" / "Invalid database" error!
    A: You likely haven't installed anything from eShop or other locations before. You will need to go to the "Nintendo 3DS/<id0>/<id1>/dbs/" directory on your SD card and create empty "title.db" and "import.db" files. Then, go to System Settings -> Data Management -> Nintendo 3DS -> Software on your 3DS and let it repair the database files.