The Toblerity project is a http://github.com organization that contains a number of related Python projects for manipulating, querying, and processing geospatial geometry data.
Shapely is a Python wrapper for GEOS for algebraic manipulation of geometry.
Rtree is a Python wrapper for libspatialindex for fast spatial queries of geometry.
zope.index.rtree is a module that uses Rtree to provide spatial indexing to ZODB3