On some systems you want APC to work for a few Virtual Hosts, but not all -- as it may break things like phpMyAdmin.
You can do that by disabling the APC "cache_by_default" option globally. In your apc-config file (usually /etc/php.d/apc.ini or somewhere along your general /etc/php.ini file) you disable the default caching.
apc.cache_by_default = 0
And you can then enable it per Virtual Host you like, either in the general Virtual Host apache config or in the .htaccess file if you allow Overrides in the Apache config.
php_flag apc.cache_by_default On
Notice the difference in the apc.ini config where the value is set to '0' (zero). When passing "flags" to PHP via the Virtual Host or .htaccess config, it's either On (=1) or Off (=0).