Mark McWilliams has a handy post on his site which I found quite useful on upgrading my WordPress installation here to 3.1.  It’s about the new archives for custom post types.  I had been using page templates with queries which worked fine but had some bugs.  Namely being inconsistantly applying current page css for the custom post type archive templates.  Following his little guide, I was able to delete my pages, rename my templates to archives, and remove the queries.  Then I just used custom links in my menus to link to the new archives.  It works great and solved all my issues.  If you’ve been using page templates to list your custom post types I highly suggest you read up and get ready to switch over.  It only took me a few minutes.