Almost-Delauanay Tetrahedra (AlmDel)
For analyzing protein structure

Alpha Shapes
General purpose software for analyzing protein structures
Ciel
For generating interface surfaces from protein structural data.
Coreset
For computing shape descriptors of low-dimensional data sets
Monte Carlo Simulation
For performing efficient Monte Carlo simulations of proteins

ProShape
For computing protein measures and their derivatives

Skin Software: current version | original version
For triangulating the surface of a protein
Stochastic Roadmap Simulation (SRS)
For computing ensemble properties of molecular motions (folding, binding)
Writhe
For computing the writhing number of protein backbones

CGAL: Computational Geometry Algorithms Library
Computational Geometry Pages lists additional software
Geomview
LEDA
VTK: The visualization toolkit