Hi Steve, Great resource, thank you.
I was initiating several of your recommendations in regards to php.ini and .htaccess hardening after experiencing an attack that left a couple of malicious php files on my server - files that purpose was to fool Googlebot into seeing different content and links than the public see. Luckily I caught it early enough through Google Webmaster Tools, but I'm now more aware of the issues that can allow this to happen. In my case the doorway was an installation of OSCommerce that had not had all the precautions recommended for that script in place.
Anyway a comment about the section of Rewrites for .htaccess
RewriteCond %{QUERY_STRING} ^.*=(ht|f)tp\://.*$ [NC]
# Allow yourself, for SMF Forum Package Manager upgrades.
# Set it to your own IP address so you are the only one who won't be blocked.
#RewriteCond %{REMOTE_ADDR} !^111\.222\.333\.444$ [NC]
RewriteRule .* - [F,L]
RewriteCond %{QUERY_STRING} (\?|%3F) [NC]
RewriteRule .* - [F,L]
I couldn't get any of these to work until I remembered the line that needs to precede them
Rewrite Engine On