Software

VisTrails: VisTrails is a new scientific visualization system that enables scientists to keep track of their visualization and simulation pipelines as the problem domain and dataset changes. VisTrails stores provenance information for the pipelines - the entire version tree. Interactively comparing results of different versions allow scientists to dramatically increase productivity. Additionally, since VisTrails pipelines are actually execution specifications, VisTrails makes it easier to reproduce and compare results of previous runs.
Afront: afront is an advancing front mesher that constructs nicely shaped meshes from point clouds, bad meshes and implicit surfaces. Afront is the base code for the SGP'05, EG'2006 and Vis2006 papers. Afront is developed and maintained mostly by John Schreiner and myself.
HAVS: Hardware Assisted Visibility Sorting - to the best of our knowledge, HAVS is the fastest GPU tetrahedral cell rendering software out there. HAVS is written primarily by Steven Callahan.

Python bindings for teem. Teem is the swiss-army knife of volume manipulation tools. Since Python is the mother of all glue code languages, it only made sense. Get Python-Teem here - hosted at Google Code.
Szymon Rusinkiewicz has written a fantastic library called trimesh2 for manipulating and viewing meshes. I've made some changes to it so that I can generate reasonable-looking screenshots, and some other assorted things (like converting to our internally used file formats, and sampling points from a triangle mesh). The patched version (patched against trimesh2 2.7) is available here. You'll need ImageMagick on your path to get the nice screenshots. Press 'p' and a digit d, and you'll get a 2^d * 2^d supersampled screenshot, courtesy of convert and montage.

My .emacs. Beware -- here be dragons.
.emacs_common. Random functions. Same warning applies.
python-find.el: python-find.el helps you search for strings in collections of python files in a convenient way.
python-selective-display.el: python-selective-display.el takes advantage that python's indentation matters to make Emacs' selective display useful.
case-convert.el: case-convert.el makes it marginally less painful to convert from camelCase to camel_case.

PGHFlow: PGHFlow is the software I developed for my undergraduate thesis. It solves the 2D Navier-Stokes equations on the GPU using a method known as SMAC. Unlike Stam's stable fluids (which are unconditionally stable and thus suitable for real-time applications with unboundedly large timesteps), SMAC is only conditionally stable (in particular, subject to the CFL conditions). However, SMAC produces results that agree with fluid experiments, and so is suited for engineering applications. Alas, bitrot has claimed PGHFlow, like most GPU-based code that goes untouched for more than a couple of months.