Update (2008-01-21): See http://pypi.python.org/pypi/Shapely/1.0.
An older, slightly outdated, post of mine about Python geometry packages is getting read enough to warrant an update.
Geometries from mapscript.py and ogr.py haven't changed in the past year. The GeoDjango developers are finding that the geometry API in geos.py isn't so bad -- perhaps because they're doing the bulk of their operations and transforms within the database -- but the fact remains that the GEOS project is trying to deprecate use of the C++ API, and that this puts geos.py in some peril.
Since the Python Cartographic Library's 0.11 release, geometries are now a part of the PCL-Core component's cartography.geometry package. Howard Butler added pickle support, and we've fixed a number of bugs since the start of 2006. We've also reduced the dependencies of PCL-Core, as you can see in INSTALL.txt. Remember, "zope" is now a namespace package, and you can install zope.interface [Cheeseshop] separately from any other piece of Zope 3.
I have nothing to report about FDO's brand new geometries for Python. My understanding is that they are also based on GEOS.