The Wiki system that's coming in 0.97 will allow us to name worlds - and I can see that being expanded to allow us to place markers on the surface to name locations. It's just a lat/long coordinate and a name, after all.
I assume with most of it being procedural it might have an issue.
It's not as big an issue as you'd think. As I understand it, everybody's computers generate the same procedural planets as each other, so, as long as you are running the same version (and without any differing mods to the galaxies or the algorithms) as whoever discovered, named, and mapped the planet, you'll see more or less the same geography as they did.
I'm not sure if the Wiki will start "saving" star systems that are entered in it, so that they remain persistent from one version to the next, or in the face of universe-altering mods... that'd be kinda cool, though I can foresee it getting bloated and affecting performance when enough systems are charted in the Wiki.