Updated revision from D2088:
You can enable specific jails in /etc/rc.conf via jail_list="" and the order in which you list them affects the order they are started. However, the order is not reversed during shutdown which can break dependencies between jails/services and prevent a clean shutdown of a user's environment.
A proposed switch could be added to rc.conf to enable the jails to stop in reverse, but not for invocations of the form "service jail stop j1 j2 j3"
jail_reverse_stop="YES"