Our first EE-powered newspaper went live on Oct. 1 at www.northwestnavigator.com. The design isn’t cutting-edge but it certainly made the client happy (U.S. Navy). The templates were designed to help us work with the print version’s 3 zoned editions.
I used a single blog for all news content, choosing instead to separate by category. The reason behind this is that I intend on using my single EE install for more newspapers so we can share basic embedded templates (like story layout) and boilerplate content (like the About Us, copyright statements, and privacy policy statements). Each future newspaper will be another blog in the system. We can also quickly build aggregate news sites by region this way (say, all papers in one county on one county-wide news site, or a state-wide election site with content from all of our papers).
Adding content from different categories on the main page was a simple matter of using multiple exp:weblog:entries statements and defining the scope of each statement to a specific category (category=“xx”).
As for custom display of the lead story, I posted my experience in this thread. Rather than use a custom field, we used a custom status since we weren’t using status for anything else and it didn’t require any special queries.
The hard part was abstracting the templates enough that they could be easily used by any other newspaper in our company and building generic enough embedded templates. I found the Snippets plug-in absolutely essential for this.