I just found out that you could run pico-8 games with fake-08 which is really cool! Other things I've done include using Tiny VNC to stream a desktop and EasyRPG player for RPG Maker 2000/2003. I've also seen someone install linux at one point.
What other cool or underrated things you could do on a homebrewed 3DS besides the usual play 3DS/DS/GBA games for free?