Structural Biology Software Database - NIH resource, at UIUC
Bioinformatics software - a so-so list of lists, at compbiology.org
Biocatalog - at EBI
Michael Smith Genome Sciences Center - mostly for sequence assembly

EBI FTP Site - miscellaneous materials, at EBI
Indiana University / Biology Department - Mac, VAX, and DOS software
National Institute of Genetics (NIG) - Mac software, including MacPlasmid and Speakquencer

BioPerl - open source Perl tools for bioinformatics, genomics and life science research
BioConductor - open source software project for the analysis and comprehension of genomic data