The "Integrating influenza antigenic dynamics..." paper has just been published in eLife. I was super impressed with pretty much every aspect of their publishing process. On the review / editorial side, I found them to be quite timely and the editor in charge of the paper was very clear about which reviewer criticisms were the important ones that needed to be addressed before the manuscript could go forward to publication (the review dialog is available in the online version of the paper). The actual submission process was extremely easy. Initial submission is a single PDF, no need to capture supporting figure metadata as with PLoS, etc... They don't enforce any particular citation format, instead capturing citations and reformatting algorithmically. Also, the LaTeX processing was quite smooth.
I also found many of their publishing innovations to be quite astute. For example, they allow and encourage data to be associated with specific figures, so people aren't stuck trying to eyeball values off a bar chart for follow up analyses. Additionally, they require that new primary datasets associated with a study be deposited in an actual data repository, instead of relying on supporting information. The data associated with this paper has been deposited with Dryad, where it gets a permanent DOI, etc... I also really like their presentation, both the web and PDF versions.