The Precedings forum on Nature Network has a small list of journals that accept / don't accept preprints.
The Romeo database contains a comprehensive list of journal pre/post print policies. A quick survey produced this list of relevent biological publishers. Feel free to add any more - Mike June 26 2007
Journal policies toward preprint servers as of June 2007. Policies quoted from the linked websites.
Duplicate content
The Nature journals allow and encourage prior publication on recognized community preprint servers for review by other scientists in the field before formal submission to a journal. The details of the preprint server concerned and any accession numbers should be included in the cover letter accompanying submission of the manuscript to the Nature journal. This policy does not extend to preprints available to the media or that are otherwise publicised outside the scientific community before or during the submission and consideration process at the Nature journal.
Nature journals allow publication of meeting abstracts before the full contribution is submitted. Such abstracts should be included with the Nature journal submission and referred to in the cover letter accompanying the manuscript. This policy does not extend to meeting abstracts and reports available to the media or which are otherwise publicised outside the scientific community during the submission and consideration process.link
Embargo
Nature journals do not wish to hinder communication between scientists. For that reason, different embargo guidelines apply to work that has been discussed at a conference or displayed on a preprint server and picked up by the media as a result. (Neither conference presentations nor posting on recognized preprint servers constitute prior publication.)
Our guidelines for authors and potential authors in such circumstances are clear-cut in principle: communicate with other researchers as much as you wish, whether on a recognised community preprint server or by discussion at scientific meetings, but do not encourage premature publication by discussion with the press (beyond a formal presentation, if at a conference).
This advice may jar with those (including most researchers and all journalists) who see the freedom of information as a good thing, but it embodies a longer-term view: that publication in a peer-reviewed journal is the appropriate culmination of any piece of original research, and an essential prerequisite for public discussion. link
Confidentiality
Contributions submitted to or in press with a Nature journal must not be posted on any web site, except for preprints posted on recognized preprint servers (such as ArXiv) where this is community practice. The server concerned must be identified to the editor in the cover letter accompanying submission of the paper, and the content of the paper must not be advertised to the media by virtue of being on the preprint server.link
Other Nature journals seem to follow a similar policy, for example Molecular Systems Biology states
“Submission of a paper implies that it reports unpublished work and that it is not under consideration for publication elsewhere. Molecular Systems Biology allows and encourages prior publication on recognized community preprint servers for review by other scientists in the field before formal submission to the journal. The details of the preprint server concerned and any accession numbers should be included in the cover letter accompanying submission of the manuscript. This policy does not extend to preprints that are publicised outside the scientific community before or during the submission and consideration process at Molecular Systems Biology.”
However it's probably worth checking with the journal you are planning to submit to before hand.
Any manuscript, or substantial parts of it, submitted to the journal must not be under consideration by any other journal although it may have been deposited on a preprint serverlink.
As to pre-print servers we run the same policy as the rest of PLoS, which is to allow publication of papers versions of which have appeared on a pre-print server. Thanks to Pedro for questioning Plos in their forum. link
Full list of OUP life science journals
For the majority of Oxford Journals, prior to acceptance for publication, authors retain the right to make a pre-print [A preprint is defined here as un-refereed author version of the article] version of the article available on your own personal website and/or that of your employer and/or in free public servers of preprints and/or articles in your subject area, provided that where possible.
You acknowledge that the article has been accepted for publication in [Journal Title] ©: [year] [owner as specified on the article] Published by Oxford University Press [on behalf of xxxxxx]. All rights reserved.
Once the article has been published, we do not require that preprint versions are removed from where they are available. However, we do ask that these are not updated or replaced with the finally published version. Once an article is published, a link could be provided to the final authoritative version on the Oxford Journals. link
PNAS considers results to have already been published if they have appeared in sufficient detail to allow replication, are publicly accessible with a fixed content, and have been validated by review. A paper has surely been published if it has appeared in a journal cited by any widely used abstracting service, whether in print or online, in English or in any other language. Gray areas result when two of the three criteria (replicability, public accessibility, and review) are met or only a portion of an article has appeared before. What if only one figure has been published previously? That need not doom subsequent publication in PNAS, but the authors must convince us at the time of submission that the figure is essential for the submitted paper yet not the major contribution.
Preprints have a long and notable history in science, and it has been PNAS policy that they do not constitute prior publication. This is true whether an author hands copies of a manuscript to a few trusted colleagues or puts it on a publicly accessible web site for everyone to read, as is common now in parts of the physics community. The medium of distribution is not germane. A preprint is not considered a publication because it has not yet been formally reviewed and it is often not the final form of the paper. Indeed, a benefit of preprints is that feedback usually leads to an improved published paper or to no publication because of a revealed flaw. Analogous to a preprint is the often detailed oral presentation of work at a conference. Once again we do not view this as prior publication but as a salutary step toward publication. link
The journal only accepts papers that present original research that has not been published previously. Submission to the journal implies that another journal or book is not currently considering the paper. Submitted manuscripts must not be posted on any web site and are subject to press embargo.link
Prior publication Science will not consider any paper or component of a paper that has been published or is under consideration for publication elsewhere. Distribution on the Internet may be considered prior publication and may compromise the originality of the paper as a submission to Science. Please contact the editors with questions regarding allowable postings.link
Manuscripts are considered with the understanding that no part of the work has been published previously in print or electronic format and the paper is not under consideration by another publication or electronic medium. link