You can rename ships, fleets, and planets. Might be able to rename unit Groups, not sure on that, however.
The system I use is to simply go from right to left on the galaxy map and check everything (sometimes I will do war fronts first, then go through each system). If I leave the game for a length of time and want to remember to do something, I just stick a Post-It on the edge of the monitor with the reminder. I don't use the System Notes feature, since I find it a bit more tedious than the SE3 system (right click, notes, and that's it... I never really used the notes in SE3 though either, never was much need
).