Yes, I've created such an exe with py2exe (and more recently with cx_freeze). This exe has been used successfully on multiple machines and it uses h5py heavily (through
https://pypi.python.org/pypi/h5pom). An example with the basic script & setup.py follows. You should likely reply with more details about what "crashes at run time" means if this is not helpful. If it gives you a traceback about missing modules then its likely that this reply will help you. If it segfaults (hmm, I mean the windows version of that!), then there's something more interesting going on. Figuring out the includes and excludes for py2exe I find to be a rather black art of trial & error.
--- h5py\example.py ----
import h5py
f=h5py.File("package_test.h5")
f.close()
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--- setup.py ---
from distutils.core import setup
import py2exe
# h5py example
# NOTE: h5py needs numpy so this builds on the numpy example
options = {}
options["py2exe"] = {"includes": ["h5py.defs", "h5py.utils", "h5py._proxy"],
"excludes": ["h5py.ipy_completer", "IPython", "Tkinter", "tcl"]}
setup(console=[r'scripts\h5py_example.py'], options=options)
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