@Seiya
If you have ixemul environment and gcc set up, that'll work just fine (sh configure or from sh itself: ./configure), assuming no unsupported functions are used. Many things will build out of the box with ixemul. Sometimes you'll need to fetch and build some libraries before you can build some more complex application, though.
Also, in some cases you might need to update two files (
config.guess and
config.sub) before configure will work.
This is the easy way to compile things. If this works you might want to try adding -noixemul and see if the thing builds with libnix (that is without requiring ixemul.library to run). For simple programs this will work aswell.
If the program has GUI or somesuch, then you're pretty much forced to rewrite large portions of it.
In case you're asking about amiga specific sources: These often use just makefile and make (smakefile/smake for SAS/C, makefile/make for GCC). Anyway, there is no set rule for this, every project can have a different build system.