Well, yes, the original question was about a system with no fuel source. But since the answer to that was basically "tough luck", i'll have to settle for the second best, and try making depots nearby.
And no, the issue is not protecting the mine.
It's usually about backwater colonies and stuff like that. Places of no particular strategic importance, that can still be struck by pirates (and usually are, magically the very second, when the assigned fleet leaves for fuel... such coincidence);
Places, where i am not active at the moment, and therefore can not go for the more micro-managy solutions.
And the advantage of assigning fleets to these positions, instead of (or rather in addition to) stationary defenses, is, that i end up having mobile fleets on station across my empire, often close enough to regroup and help, if something really serious goes down.
Call it strategic reserve.
The "valuable" bit of Sharks7 answer was the part about leaving out the commerce center, to make the base exempt from the normal private economy - this, while might seem obvious to some, is something i hadn't thought about myself.
As I mentioned earlier. Having reserve fleets ready to redeploy is necessary. As one fleet goes back to refuel and Repair, the Reserve fleet redeploys to the front.
I have my fleets divided into Main fleet and Anti Piracy Fleets or Patrol fleets of 5 -7 Ships each. They are faster to repair, consume less fuel as compared to larger fleets and can move around a lot faster. When you take into consideration the time required for a fleet of 25-30 ships to repair and refuel.
If you get into a shooting match with another empire. You can send these same smaller fleets to target their refueling hubs...
In short, move in with your reserve fleet into the contested zone. The send your other fleet for refueling repair, upgrade etc....