pyCGNS
Python interface for CGNS (data standard for computational fluid dynamics). [Open Source, GPL]

PyDaylight
Turns the Daylight toolkit into a rapid application development system for chemical information by providing a full Python interface. [Open Source, LGPL]

Pmv, ADT and ViPEr
Python software from the Molecular Graphics Lab (MGL) of the Scripps Research institute. [Free for non-commercial use]

PySomorph
A python package for investingating subgraph isomorphism.

The Biopython Project
Freely available Python tools for computational molecular biology.