PieTree
PieTree is a program for producing pictures of phylogenetic trees, particularly for the purpose of displaying ancestral state reconstructions of discrete characters. For more details, examples, code to download, and a link to a web demo, please see the PieTree page.
SimTreeSDD
SimTreeSDD is for batch simulation of phylogenetic trees under state-dependent diversification. To go along with it is code for maximum likelihood estimation of character change parameters under a flexible variety of constraints. I don't have the code packaged up yet, but email me if you're interested, and I'd be happy to share.
edgefx
edgefx is an R package for computing the ecological effects of habitat edges in landscapes. I wrote it for Leslie Ries, and it will be available towards the end of the year.