protCAD - as a Ph.D. student with William F. DeGrado at UPENN I wrote a library of object-oriented general-purpose protein modeling and analysis tools (in C++), primarily used for de novo protein design. My focus has shifted a little bit since I've left the lab, and I'm currently working with and developing a variant of the code for both protein structure prediction and design.

Useful Software On The Net

GROMACS - The fastest, most obsessively optimized molecular dynamics code on the planet!

Object Oriented Numerics - A fantastic site dealing with object-oriented numerical computing, also contains links to freely available and commercial packages.