Hi. I've just upgraded to WP3.0 on my test site and discovered a problem with category archives when pretty permalinks are on. A top-level category archive (eg http://test.londonkoreanlinks.net/category/dprk/ ) works just fine, but a second-level archive (eg http://test.londonkoreanlinks.net/category/dprk/voice-of-dprk/ ) gets a 404 result.
I tried it on several themes, to make sure it's not an incompatibility of my theme framework, and it's the same problem on all themes I tried. I also tried switching to the default permalink structure and then switching back to pretty permalinks to see if things just needed flushing out (as is necessary for example when switching on custom taxonomies) but that didn't resolve the problem (eg, the second-level category archive noted above works fine with the default permalink http://test.londonkoreanlinks.net/?cat=12 ).