As a rule of thumb, if something is console-only, you use ixemul. If something opens a window, you must never use ixemul.

So for a console tool, especially if it interacts with bash scripts/makefiles, you use ixemul.
If you need compatibility with linux paths, you use ixemul.

If you need any sort of a windowed UI, you use libnix.

SDL ports must use libnix.