My system uses peer to peer software to synchronize each container's public keys and IP address/port information, as well as a mesh network VPN. This allows me to easily join a new node to the VPN cluster (using ENV variables to specify the port and public address to listen on, which is then used in the Docker container creation) and still have minimal latency between any two nodes.

I'll probably have to write up a post myself describing the system and how Docker is used to create new containers and add it to the cluster.