Biodiversity and Biological Collections Software
BioLink
BIOTA: The Biodiversity Database Manager
DELTA/Intkey
Digital Taxonomy: A Web Resource for Open Source Biodiversity Informatics
EarthCape
EMu
Freezerworks, Dataworks Development, Inc.
Iowa State Entomology Index of Internet Resources
Lucid
Mantis
Papis
Papyrus
Specify: Biodiversity Collections Management

Morphology and Imaging Hardware and Software
Auto-montage
CombineZP
Digital Morphology
HeliconFocus
people.html Integrated Morphometrics Package (IMP)
Morphometrics at SUNY Stony Brook
StackShot
Visionary Digital
Zarbeco
Zerene Stacker

Phylogenetics Software
CIPRES Science Gateway
Evolutionary Biology Group: Software, Department of Zoology, University of Oxford
Felsenstein's list of Phylogeny Programs
Goloboff's programs for cladistics and biogeography
Indiana University archive of Molecular Biology Software (IUBio): link 1, link 2, link 3
Molecular Evolution, Phylogenetics and Epidemiology Research Group: Software
MrBayes
POY (Phylogeny Reconstruction via Optimization of DNA and other Data)
RAxML
Rod Page's software programs and list
softlinks: Kolokotronis' list of Evolutionary Genetics Programs
Winclada/Nona/TNT