JJ's site has always been simple. It's kind of nice without having to navigate all through the junk to get to the point. That's the big huge problem with pvp. In order to really even get to the comic you have to often scroll through boring chat text and the author talking about things not even related to the comic in any large way. it got me to stop reading.
I like the Penny arcade or Dominic Deegan (
http://www.dominic-deegan.com) approach to comics. Frankly it's simple and leaves room for links and comments but you can still easily click in and read the comic and click out without having to scroll through a blog or ad banners to do so.
Basically put just keep it simple.
edit: Before I forget Maybe having a small bar of text under the comics with links to essays and JJ's blogs would be nice. Just a very small banner or something. A lot of the essays are rather intersting so easy navigation to them would be kind of cool