The master branch of this repository (https://github.com/Drenn1/GameYob) currently contains the source for an unfinished overhaul of GameYob after release 0.5. In particular, this overhaul allows for the emulation of multiple gameboys, in order to improve wireless link cable emulation by emulating both gameboys on both systems. It also facilitated the 3DS port (and SDL for testing purposes).
However, because speed suffered slightly and kinks were never fully worked out, no public releases were made with this branch. Updates were instead done on the "v0.5-hotfix" branch to fix issues with GameYob version 0.5.
Also, despite some residual 3DS code in this repository, SteveIce's fork for the 3DS version had far more work done on it. That repository is down now, but a fork can be found here: https://github.com/ZopharsDomain/GAMEBOYC-3DS-GameYob
The 3DS version had its own kinks, which means you may still prefer to use the DS version even on a 3DS. It is recommended to install it using the DSiWare CIA file provided with the newer releases of GameYob DS.
See the GBAtemp thread for more information:
http://gbatemp.net/threads/gameyob-a-gameboy-emulator-for-ds.343407/