Did your user’s theme options and widgets page disappear?
Well here’s a little bug that was discovered, though it’s not really a bug in WordPress itself, rather a change. It shows up in themes with higher-level capabilities attached to certain menu items.
In 3.0, this was made more stringent with the merge. the theme editor was left in with only Super Admins having access to it. Regular site administrators should not have access.
Some themes, however, have additional menu items (options pages) that use the capability edit_themes to access.
If you find this is happening to you, just search the theme’s functions.php file and change the edit_themes cap to edit_themes_options. That should fix it.