Recently, I participated in a "hackathon" sponsored by NEScent, the National Evolution Synthesis Center. The goal of this weeklong meeting was to gather together programmers who are writing comparative algorithms in the r software language.
If you haven't discovered r yet, it's a free and very powerful platform for carrying out all sorts of statistical analyses. r syntax is a little difficult to master, but it is really worth learning. You can download r here, and find free documentation to learn the language here.
The great thing about r is that people have written all sorts of useful packages to do various things. Most of the phylogenetic comparative approaches available in r are based on Emmanuel Paradis' ape package. My package, geiger, for example, is dependent on the framework provided by ape.
The point of this post, though, is to point out that the hackathon produced a product of great usefulness to the community: the R-phylo wiki. This wiki has detailed instructions for carrying out all sorts of comparative analyses, from independent contrasts to disparity-through-time, in r. Enjoy!