For anyone who hasn’t found it through other means, if you upgrade to WordPress 2.6 and you use a custom permalink structure (aka “pretty permalinks”) as I do, there’s a bug. To be specific, if your permalink structure includes a reference to your index.php file, they will no longer work. The workaround is to edit/create your .htaccess to use mod_rewrite and remove index.php from the link, as described here.
I’m not a big fan of using mod_rewrite, but it’s the only workaround to maintain pretty permalinks with WP 2.6. The WP gods are aware of the problem and are determining a proper fix for the next release, but given the workaround, it’s been deemed non-critical.