I noticed that wp-settings.php in 2.9.2 was almost twice as large when I was investigating why the authentication cookies (wp_logged_in...) where not set. We are bypassing the normal wp-login.php by shibboleth authentication and in 2.9.2 the cookie was ok since COOKIE_DOMAIN was set there (in wp-settings, thus known in pluggable.php where the cookie is set).
Where is COOKIE_DOMAIN defined now ? Or there other settings that we should check after this 2.9.2 to 3.0 upgrade ??