I often use a setup script that is used for normal distributions as well 
as py2exe distributions
I have added the ideas below to the wiki page, others may find it useful 
or have better ideas :-)

http://starship.python.net/crew/theller/moin.cgi/PassingOptionsToPy2Exe


  2 Avoid using setup parameters that are py2exe-specific

Instead of passing options like console, windows to setup(), you can 
subclass Distribution and initialize them as follows:

from distutils.core import Distribution 
class MyDistribution(Distribution): 
    def __init__(self, attrs): 
        self.com_server = [] 
        self.services = [] 
        self.windows = [] 
        self.console = ['myapp'] 
        self.zipfile = 'mylibrary.zip' 
        Distribution.__init__(self, attrs) 
 
setup(distclass=Distribution) 



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