> shapely's installation instructions from windows are to use 
> chris gohlke's prebuilt binaries from here: 
> http://www.lfd.uci.edu/~gohlke/pythonlibs/

Christoph Gohlke's Shapely‑1.5.9‑cp27‑none‑win_amd64.whl includes a version of geos_c.dll that has the VC90 manifest embedded as resource 2, just like python27.dll. The DLL also exports a GEOSFree function, which is what shapely actually uses. That said, the geos.py module still defines a global free() using cdll.msvcrt.free. As far as I can see, it never actually calls it. Otherwise it would surely crash the process due to a heap mismatch.

Steve, since you haven't closed this issue, have you considered my suggestion to export _Py_ActivateActCtx and _Py_DeactivateActCtx for use by C extensions such as _ctypes.pyd? These functions are better than manually creating a context from the manifest that's embedded in python27.dll because they use the context that was active when python27.dll was initially loaded.