Now, the 3DS has just received a new piece of homebrew called uae3DS which is a port of uae4all letting you emulate the Amiga 500.
This port, which was released by Badda this weekend, is currently work in progress but performance is said to be pretty good on both the Old and New 3DS which allows many titles to be playable according to the developer. In the future, there are plans to add quite a few features including:

  • A CIA version
  • Some form of auto-updater presumably making use of an internet connection
  • Keyboard and mouse functionality on the bottom screen
  • Key mapping with the ability to save combos to SDCard
  • Autofire functionality
  • An option to get rid of black borders and do screen scaling/zooming
  • Other stuff like moving the status bar to the bottom and attaching/mounting a directory on the SDCard as an emulated hard drive

You may read more about uae3DS and find its download links on its GBATemp thread.