I only noticed today BMC also had a Systems Biology journal. There are no papers yet but the editorial board looks interesting enough. From the types of articles they expect I think they will take a lot of bioinformatics related manuscripts. This adds to two other Systems Biology journals that I am aware of: Molecular Systems Biology (also open access) and IET Systems Biology.
(via BioHacking) On a more creative note, here is the Journal of Visualized Experiments. It is a "journal" of recorded experiments that should help others learn protocols with the aid of videos. Currently the submissions are subjected only to editorial evaluation and are expected to get published in about 14 days. They plan to apply for listing in PubMed and other databases.
The videos are accompanied by a very short written explanation and are tagged for searching. There are no comments or RSS features that I could see.
Nature Methods and Nature Protocols should give this a try. By the way, Nature Protocols also publishes protocols in bioinformatics, and Nature Methods started a blog (Methagora)
With this continuing expansion of journals in all publishing houses aren't we quickly reaching a point when manuscripts will be the scarce resource ? I really hope someone develops nicer tools to suggest communications to read based on my interests. Is there a place for researchers whose job is just to associate and shuttle communications around ? Tagging communications as FOR_SMITH_J to show up in some reader with a comment: "solves your problem X".