I was looking for modules able to merge or intersect shapefiles. shapely is probably a good place to start but I was surprised to discover others modules extending shapely in their own way.
descartes explicitely extends shapely
fiona leverages GDAL
geopandas tries to unify all of them
mapnik: binding for Mapnik
pyproj leverages PROJ.4 to convert geocoordinates into many projections systems (list)
shapely leverages GEOS