Definitely name them BTW - I love this game, but the default naming scheme for, well, anything but planets sucks - {G}.
I generally have One rally point permanently 'assigned' at every starbase so I can drop constructors to them for upgrades, one for every planet I have consistently running colony ships outward (Just change the rally point to your new planet as needed, and one going for any natural 'groupings' of manufacturing worlds that produce fleets.
They're also useful as map'notes' for strategic objectives you know you're going to want to grab later "Mine-inf-Carinoids", "Rest.-Thalan",
Jonnan