Huh, strange. My standalone build sucked in numpy and PyQt4 (but not PySide) no troubles at all. I did have a minor problem with ctypes (explicitly importing _ctypes was required), but apart from that surprisingly smooth sailing. I have tried Cython briefly but Nuitka seemed a lot easier; just point and go. No modification to the source code needed and I ended up with a nice .exe and a bunch of .dll and .pyd files (including those for numpy and PyQt4). Build time was 30 minutes for a small-medium size application (25000 lines) in Python 2.7.