To elaborate, what I am imagining is a "mark system" button/hotkey that places a flag on the next star system I click on. That flag could be an actual icon adjacent to the system, a change in the coloration of the text, whatever; the important thing being that I can control the color of the flag when I place it (perhaps a dialog or popup would open upon placement). In the preferences, I should be able to associate a bit of text with each color; that text should be visible as hovertext.* If I could have a way of attaching colored flags to my star systems I'd be thrilled. (Bonus points if the flags have a customizable comment.) I could use this for so many things-- check back later, send a colony ship here when I get one, this system has no planets so stop clicking on it, etc etc.
This would have a similar effect to stickies or thumbtacks on a map. Players could use them for a great many things, and it would go a long way to eliminating one of the great hassles of RTS games-- having to *remember* so danged many details about the game-state.
I don't think that the flag concept would need to be applied to fleets, since it is already possible to attach text via the rename function.