For some unknown reason for the admin user of our Moss site (and all other users who had full control permissions) the Site Action -> Site Settings menu option have disappeared from the home page. I can navigate to it by going to mysite/_layouts/settings.aspx but I can't change anything it says I do not have permissions.
IF the user logged IS the Site Collection administrator and still gets theses access denied messages, your Content Database seems to be locked. This happens during backups or when backups go wrong (get interrupted for example)
stsadm -o getsitelock -url http://server_name
if it is not showing as 'none', it is locked. fix command:
stsadm -o setsitelock -url http://server%5Fname -lock none