This is an attempt to learn what other people do with rally points.  Here's the tricks I use.

Marking Pirate bases.  I put a rally point in the tile NE of the Pirate base.  I leave the name generic.  This lets me know visually where the base is for civilian traffic to avoid, even if I don't have the base in view at the moment.  Later, when I have an initial military, the rally point list becomes a series of clean up/training missions.

Marking Space Monsters.  I put two rally points next to the base.  This visually marks the difference between a Pirate base and a Monster base, even when zoomed out.  I could use and rename one rally point, but I am lazy and the visual difference is useful.  It is pretty easy to spot these double rally points on the map, so it doesn't seem necessary to search for them in the list.

Marking Precursor Artifacts.  My early explorers cannot handle the Pirates guarding these Artifacts.   Those artifacts are, however, a prime candidate for the clean up/training crews.  I find it useful to rename these rally points for identification in the list.  Because I am indeed so lazy, they are labelled p1, p2, etc.  

Actual Rally Points.  I really don't do this a lot.  I tend to use a lot of individual auto paths and manual driving for ships, especially if I do not feel I have the areas involved cleaned out of enemy or pirate units.  I have two cases of named rally points that can come up in my games.  One is "War".  It is used to set up a fleeting area where warships and transports can gather and be sorted into proper fleets.  The click sequence for a newly created ship becomes "Go to", "War".  As needed, this rally point gets moved around.  If I get stuck in a multiple front war, I am likely to be doing a lot of manual driving, so I have never gotten to use a second combat rally point name inspired by General Sherman.  If the game is peaceful at the moment and I am just gathering a "defense force" [note sarcasm], then the rally point is named either "here" or "there" depending on how I feel at the moment.  I once got criticized by my OCD son that "go to" "here" didn't make semantic sense.  He didn't note the sarcasm.  

So, what do you do when you're all alone with your Rally Points?