Including packages that aren't automaticly detected is easy: just add the missing modules to your setup.py file:
setup(
...
options=dict(
py2app=dict(
includes=["module1", "module"],
),
),
...
)
I don't know why CFNetwork isn't automaticly included, the code for cfreactor shouldn't confuse py2app this way (that is, the imports are done using regular import statements and aren't hidden in C code or import calls).
Can you reproduce that problem using a small sample project (for example a trivial SystemPreferences plugin)? That would make it a lot easier to debug the issue.
Also, which versions of Twisted, PyObjC and py2app do you use?