Given the complexity of the publishing landscape, I thought I would say a few things about our lab preferred publication policy.
Preprint Servers. We have been enthusiastic users of the BioRxiv preprint server since its inception. Many of our papers are posted on BioRxiv before publication and there are even a couple of preprints on there that have never been published in peer-reviewed form. We don’t always post preprints – sometimes we just don’t get around to it, but the lab strongly supports the idea of preprint servers as a means to disseminate research more rapidly and as a complement to slower process of peer-reviewed publication.
Open Access. We have a strong preference for publication in proper CC_BY open-access publications.
Elsevier. Whilst there is a problem with all for-profit journal publishers, Elsevier seem especially evil. They make universities sign non-disclosure agreements which prevent us from knowing how much is being paid for library subscriptions. They have also sent me take-down notices asking me to remove pdfs from my website. So if at all possible, I avoid publication, peer-review or editorial services for Elsevier journals. A few years ago I resigned from Cell Reports Editorial board.
Double-Dipping. Many subscription journals also offer an open-access option, which can be extremely expensive. This is essentially double-dipping by publishers who are also charging libraries for the same journals. I resent paying these charges – although this does conflict to some degree with the preference for open-access publication. Perhaps the best solution is to avoid all for-profit publishers, but that would rule out a large majority of the journals that we commonly read, so I have not adopted that as a blanket policy.
Society Journals. Some society journals (notably the Royal Society) are published as not-for-profit and all funds are returned into science. This is great. Others, such as Evolution and JEB are published by for-profit publishers but a significant amount of money goes back into the society, helping to pay for student grants etc. So its better to publish in a society journal as compared to a regular for-profit journal.