I think it would be cool to have the possibility to have a map of area you have covered on a planet, system, and so on. With this game having multiple planets a mapping system would help keeping track of where a cave, lake, ore deposit or secret base was on a planet that you were at 10 planets ago.
I'd frankly be surprised if something like this didn't exist in game already. It'd be quite vital, especially as you said, if you say dig a deep cave to something important, or find a body of water with something interesting. But then you leave the world, and don't return for a -long- time. Maps would be kinda -vital- to exploration!
Why? The new update of Terraria is adding a minimap, that according to the teaser pics, can encompass a full world and display it completely, just like how you would see it from TEdit. If a fantasy game with barely some paper can get a map, we can get some gps lookalike. Maybe it has a progression too! You start with paper and pen, then upgrade to like a PDA, and the highest tier is a satellite that maps the entire planet automatically (That would be end game tech, so by that point you shoulc deserve that help after exploring tens of planets, if not hundreds.
I think it would be nice to be able to annotate maps or make notes on certain planets. Hard to keep track of all of them. Maybe even include a percentage explored note for each planet/system based on total surface area covered
It would nice to have a map which can be viewed and to be able to tag/pin particular parts of the maps (maybe using symbols) like the head of a race to indicate a village or dungeon and what race occupies it for example, being able to make your own notes (so you known what you've found as it easy to lose track as you continue to explore the starbound universe). Also a mini-map in the corner of the screen would nice to have but not essential