I am helping someone move their WordPress site from a (truly) wretched Dotster shared plan to a VPS.
Everything is transferred and working, except Apache is only serving physical files like index.php and wp-admin/, etc... Other directories on the site will return a 404 error.
I am guessing this has to do with Apache ModRewrite, but I am truly unsure at this point.
Halp!
It looks really like a problem with rewriting.
Overrides will make Apache look in .htaccess files. See http://httpd.apache.org/docs/2.2/mod/core.html#allowoverride
Hope it helps!