Scene member xerpi (whom you might remember for some of his work on the PS Vita, and even the PS4) just announced he was able to run Linux on the 3DS, and he released all the necessary files.

Linux on 3DS: Features

This release currently runs only on firmwares 9.2 or below. It’s a simple implementation for now. Xerpi explains he has dramatcially improved the speed since some of the earlier builds other people might have tried. The current version includes Busybox (a one executable alternative to several unix utilities such ls, cat, top…) and a Wayland compositor for graphics.

The current implementation runs on the ARM11 processor, and as such does not have access to all the functionality of the 3DS. In particular, Linux on the 3DS does not have access to the SD Card, Wifi, touchscreen at the moment. Xerpi announced he will be working on a bridge between the ARM9 processor and the ARM11 processor to bring that functionality, but this will take time.

The readme:

Linux 3DS Loader by xerpi

Installation:
1) Copy the zImage and the nintendo3ds_ctr.dtb to the root of the SD card
2) Copy the 3ds folder to the root of the SD card
3) Run 3DS Linux Loader.3dsx with a Homebrew Launcher
    User: root
    Pass: root

Linux things:
* You can start Weston by running:
    # /start-weston.sh
* You can change the input mode (keybord, mouse) by pressing SELECT


Sources:
* Linux: https://github.com/xerpi/linux
* Buildroot: https://github.com/buildroot/buildroot
* Linux 3DS Loader: https://github.com/xerpi/3DS-Linux-Loader

Download Linux on 3DS

You can download Linux for the 3DS on the original GBATemp thread here. Xerpi also gives explanations there on how to compile the sources yourself.

Source: xerpi on GBATemp, Thanks to @173210