||Bioinformatics.org: site contains various bioinformatics tools and is one of the best sites I've used.
EXPASY Proteomics Server: site for various proteomics tools. One of the first bioinformatics sites I used.
Israel Science and Technology Homepage: Biomedical: A site that lists other sites to do a variety of analysis.
NCBI: The National Center for Biotechnology Information has a variety of literature search and bioinformatics tools such as pubmed and BLAST.
TIGR: TIGR genomics institute the place made famous by Craig Venter.
iHOP:Information hyperlinked over proteins. Lets you find out all sorts of information about proteins after putting in the gene name or an NCBI accession number.
Mek&Tosj.com: This is a site made by some scientist that have written some programs for MacIntosh computers. There is a sequence viewing program and a restriction enzyme program. All programs are for OS X.
ApE-a plasmid editor: This is a freeware plasmid drawing and mapping program available for Mac, Windows and Linux.
FinchTV: This is a free sequence viewing program that is available for Windows, Mac and Linux.
Windows Molecular Biology Freeware:This is a list of freeware molecular biology software for Windows.
ClustalW2: A site to do ClustalW2 alignments.
Genomics of Transcriptional Regulation: A Cold Spring Harbor site that lists software for doing transcriptional analysis, motif finding, and other bioinformatics analysis.