http://www.webdesignerwall.com/tutorials/wordpress-theme-hacks/ – especially useful for category-specific themes, very useful when you want to simulate something like one installation, multiple blog of WordPress MU.
http://guff.szub.net/2005/07/21/post-templates-by-category/ – similar to previous link, but using a plugin. Have not checked to see if compatible with WP 2.5.
http://wordpress.org/support/topic/145264?replies=3 – header image by category.
http://wordpress.org/extend/ideas/topic.php?id=359&page=2 – discussion on how to remove category_base in permalinks.
Using WordPress to run a magazine site
http://living.cebunetwork.com/ – a good example by the same author.
http://www.themeplayground.com/the-best-wordpress-magazine-themes-available – a list of good themes, mostly free.
http://www.dailyblogtips.com/wordpress-themes/ – another shorter list.