Extra-dimensional spaces connected (to each other and the material plane) by a network of portals -- inhabited by incorporeal energy beings (wizards + ghost template) that possess "avatars" to enter the material realm -- and rule as gods... a la Stargate (actually C.J.Cherryh's Chronicles of Morgaine, most definitely the original influence for the movie -- contains all the key themes/concepts of Stargate). Outsiders as ultra-terrestrials (i.e. alien life-forms from a different dimension). Demons as some sort of exotic ET nano-tech gone wild -- chewing up vast areas of the planet (terra-forming it to suit their own ecological needs).
Dune's Bene Gesserit witches, guild navigators (psions bending reality with their mind) -- more fantasy than sci-fi (hard sci-fi anyway), but great concepts lending themselves to easy adaptation within the pathfinder rules set.
Just some ideas...