Go have a look at the PLoS websites, they have been redesigned. I like the look but the only notable changes are a box "From the Blogosphere" that currently links to the Open Access News blog (I wonder why:) and a link to "Readers Respond" on the left, that should put more emphasis on user participation. The PLoS Medicine site has some notable differences. First they include the PLoS Medicine blog on the home page and the "From the Blogosphere" links to a Guardian article. I guess that these are customizable and left to the editors to use to point out interesting things related to the journal or field. Now ... when will PLoS Comp Bio start a blog ?
Still no journal is taking in blog comments. It would be easy to use Postgenomic's index or trackbacks to let readers comments papers trough their blogs.
There is also an editorial in PLoS Biology about PLoS ONE: "ONE for All: The Next Step for PLoS"
The only new thing I got from the editorial was the concept of portals withing PLoS ONE. I would say it sounds a bit like the Nature Gateways, an area for the aggregation of papers and other resources related to a particular field or project. Sounds like a good idea. Again, they mention that at the start it will look like any other journal and that they will build on it in time, so I don't expect much in the launch day.