• DART, Stockholm Tools and Gff Tools - probabilistic modeling at biowiki.org
• Exonerate
• ATV/FORESTER
• DAS aka BioDAS

• PROMPT is a free open source tool to compare and map proteins

General resources

• Bioinformatics.org - the open access institute

The language wars

• BioPerl and the Generic Genome Browser
• BioJava
• BioPHP (former link was http://bioinformatics.org/biophp/ which appears to be inactive)
• BioPython
• BioLisp
• BioXML
• BioSqueak
• Bio Make
• Bio Haskell
• Biomedical Logic Programming discreetly avoids calling itself BioProlog
• Bio Weka: www.bioweka.org
• Bio Schemas: schemas.bioservices.net

And now for Something Completely Different (www.BioBike.org)

Compbio Linux distributions

• BioLinux

Footnote

Since biolisp.org and biobike.org resolve to the same address, pretending that they're "completely different" is extraordinarily silly -- Sergeant-Major

But biobike isn't a language, so it's not technically a part of the "language wars". -- Mungo the Cook