If you use Ant or Maven (both of which have EAR-creation services) you can create the EAR on any Java-friendly machine and deploy on any other. I developed on Windows XP for production use in Solaris for 3 years.
Make was great in its day, but makefiles rarely port well between Windows and Unix. Ant and Maven don't even care if they're run under Windows or Unix most of the time. The only OS dependencies I ever had were on my omnibus makefiles that could generate WARs, Red Hat RPMs and Sun packages, and that was only because the packaging program wasn't (usually) available except when you were running on the target OS.
An IDE is no substitute for an Intelligent Developer.