/var/run/ is basically a scratch directory that stores anything required within runtime only, so "basically" it can be completely erased on shutdown.
But some ports abuses it to have permanent directory, thus, /etc/rc.d/var_run script exists (need configuration in /etc/rc.conf).
The purpose of the script is to create directory hierarchy data and re-creates the hierarchy on boot. If I recall correctly, you'll need to run service var_run save before configuring /var/run to be tmpfs.
In my humble opinion, ALL ports that wants promising subdirectory under /var/run should have rc.d script (basically in /usr/local/etc/rc.d, as ports are not base) and create it on startup. Some may be to just created the directory if nonexistent or cleanup if any remnants remained, though.
