I always just use a systemd or open rc service to run my stuff, pretty much a shell script and voilá. As long as you know to set proper firewall rules and run things as non-root your pretty much ready.
Not only does using Docker avoid dependency hell (which is IMO the biggest problem when running different software on a single machine), it has good sandboxing capabilities (out-of-the-box, no messing with systemd-nspawn) and UX that's miles ahead of systemd.
