Somewhere between Debian “Lenny” and Debian “Squeeze” (current), the libapache2-mod-php5 package has changed slightly.
If have your web content in /home/ (for example, /home/web/SITENAME/), then PHP will be suddenly turned off – and there aren’t any clues in the logs why.
The reason for this is the following configuration:
# To re-enable php in user directories comment the following lines
# (from <IfModule ...> to .) Do NOT set it to On as it
# prevents .htaccess files from disabling it.
php_admin_value engine Off
You’ll have to comment out those lines (… just like the configuration comment says).