Isn't it redundant to have *both* a Limit and LimitExcept if all you're trying to do is limit HTTP methods for everything on a given httpd to only GET POST HEAD?
<Directory />
Options FollowSymLinks
AllowOverride None
<Limit GET POST HEAD>
Order allow,deny
Allow from all
</Limit>
<LimitExcept GET POST HEAD>
Order Deny,Allow
Deny from all
</LimitExcept>
</Directory>
