Rockefeller compilation of software.

Phylip, a free package of programs for inferring phylogenies, from Joe Felsentein of the Univ of Washington, who also has a compilation of nearly 200 software programs, mostly free, at: Phylogeny Programs.

EMBL-EBI European Bioinformatics Institute suite of tools, includes free software and good descriptions of things such as fasta, blast, etc.

Primer3 . Primer design.
Primer 3 tutorial: http://www.broad.mit.edu/genome_software/

PAUP* Phylogenetic Analysis Using Parsimony (and other methods). Not free but inexpensive ($85-100 depending on version, as of this writing) and widely used with good support. From David Swofford, Florida State U.

Computational Biology Services Unit. From Cornell. Includes freely available software.

QGene. Macintosh software for molecular marker analysis. Downloadable manual also available.
QGene Tutorial by T Fulton, IGD, Cornell University

Mapmaker. http://abraxa.snv.jussieu.fr/people/jompo/Public/MapMaker_for_Macintosh/ (for the Mac) and http://www.broad.mit.edu/ftp/distribution/software/mapmaker3/.
Mapmaker Tutorials by MIT Genome Center: http://www.broad.mit.edu/genome_software/
Mapmaker Tutorial by T Fulton, IGD, Cornell University Mapmaker Tutorial

DnaSP DNA Sequence Polymorphism, from J. Rozas et al., University of Barcelona

Biological Software, a compilation from the Pasteur Institut in France, includes sequence analysis programs, pattern searches, structure analysis etc.