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There should be a menu like the configuration menu that exists in Java, for configuring the parameters to pass to the jython invocation. I haven't found a way to pass these parameters in a per-project way.
Invoke File->Project Properties->Run and enter something into the "Application Arguments" dialog. Verified using Python 2.7.9 and Jython 2.7.0 using "print 'Argument List:', str(sys.argv)" Tested using NetBeans IDE Dev 201505170001