If your program opens a hardcoded file at "/tmp/foo.bar", then it won't work on Windows (which is why the Java cross-platform standards say you can't hardcode file paths).

Other programs may make subtle assumptions about the word size (32-bits vs. 64-bits).

Doing unlink $file won't delete the file on systems that have versioned filesystems (like VMS). In such a case, unlinking the file returns it to the previous version. You have to do while(-e $file) { unlink $file } to completely get rid of it.

Cross-platform issues are often subtle and cover a wider range of cases than any one programmer could possibly remember. The only real way to know is to try it on the platform and test throughly.