GIS - Beyond Earth

Starrynight: http://www.starrynight.com/
It's a very nice software, it displays other planets and the universe.

I found this paper too: http://www.lpi.usra.edu/meetings/lpsc2005/pdf/2213.pdf

Nasa WorldWind displays non-earth data for many planets.

As for "Are there specific software packages for handling non earth data/coordinate systems?" there is NAIF SPICE provided by JPL. This has very accurate coordinate systems etc to cover surfaces of nearly all interesting celestial bodies as well as their relative positions and motions. It's not very closely tied to GIS, as techniques to gather the data and its applications are different.

SPICE is great if you're able to program in C, Fortran or IDL but it does not provide handy GUI apps for non programmers (not last time I checked) You might find useful apps provided by various planetary science research groups, universities etc. (Beware googling irrelevant results such as for cooking, and the "spice" circuit simulators used in electronics.)