Joe Felsenstein's list of phylogeny programs:Probably the most comprehensive
Classification Society of North America: List of cluster analysis software
Genetics Software from the Slatkin Lab: Links to sites for downloading phylogenetic software.
Georg Fuellen: Multiple Alignment Resources
Glasgow taxonomy and systematics software:
IUBio Archive: Molecular evolution software
IUBio Archive: Macintosh molecular biology software
Willi Hennig Society - Education: Links to recent books, software, and resources.