From Bioinformatics.Org Wiki
Bioinformatics.Org is an international organization which promotes freedom and openness in the field of bioinformatics and is the root domain of a damned fine Website :-) .
CCP11 (Collaborative Computational Project 11) is another product of the UK's Genome Campus. To quote their Web site, it was...
"...established to foster the broad bioinformatics community and the UK research community in particular. Its purpose is to facilitate the transfer of knowledge and expertise through conferences, workshops, a newsletter and the use of the world wide web. CCP11 is funded by the BBSRC and is hosted at the MRC Rosalind Franklin Centre for Genomics Research RFCGR located on the Wellcome Trust Genome Campus, Cambridge."
BioPlanet is well worth visiting. It describes itself as "a not-for-profit site, funded with our resources, for [its users'] benefit"
ColorBasePair is a densely packed portal with lots of bioinformatics links
Nick Yates runs his own informative bioinformatics site, unsurprisingly called nick-yates.com. He doesn't aim to make money from it, but it may have paid-for ads. Check out the glossaries---they are better than mine.
The RPBS project provides free access to several software related to structural bioinformatics. An English & a French version is provided to users.