Unless I'm completely mistaken, running any *nix in UAE will be painful at best due to the MMU requirement. Last I checked MMU emulation in UAE isn't supported at all with the JIT turned on, and may require a patch even with it off, so Aranym as suggested might be the best bet if you absolutely have to use Linux m68k or NetBSD.
I hoping I'm wrong and that someone will correct me and that it's all integrated and working well just that I haven't switched on the right options (I'm running E-UAE, though, not WinUAE), because I have some experiments I'd like to do w/classic AmigaOS that requires MMU and I have also been looking at getting NetBSD running before I ran into the MMU stumbling block.
