Here's a neat 3 AM idea. Planets are already generated procedurally in Starbound; so most of the framework must already exist. One of the things which we can build, through the wiring station, are logic gates, sensors, and switches. As of the winter update, Starbound also has rigid environments which cannot be altered, at least not until the (gigantic) environment stabilization machine is switched off. This in mind: Player meets NPC in town, possibly a blacksmith or engineer. Player is presented with a specific environment, which they must find their way through. There are restrictions on which pieces can be applied to it, but a device must be made which triggers a sequence of locks and corridors through water level, timers, and so forth. At the other end of the puzzle is the victory token and quest completion.
Puzzle game quests! But given the setting of Starbound, with potentially a super-high-tech twist! That's awesome!! +1 : D