Is it okay to stack an Airport Extreme on top of a Mac mini?
Stacking is not recommended. According to the Mac Mini user guide it is not recommended to place anything on a top of a Mac Mini, since its can interfere with the Mac Mini's Antennas for Wifi, Bluetooth and optical drive operation. Additionally, since that area kind of gets hot on my Mac Mini Late 2009, its probably not a good idea to cover it, since the Mini would be adding heat directly to the bottom of the Airport Base Station as well, and it does not have fans to keep it cool. 

As noted in Mac Mini Late 2009 User Guide


  Important:  Don’t place anything on top of your Mac mini. Objects placed on top may interfere with the optical drive or the AirPort or Bluetooth®
   wireless signal.


In your case a stacking solution (pictured below) might be the safest way to save space and keep your hardware on the safe side to the written letter in the book. But if your careful and things are not interfering and things are not getting too hot, stacking might be OK, contact Apple to be certain. 

Also consider moving your Airport Extreme to another location, it might help avoid sources of wireless interference at your desk, eg monitor, computer, speakers, cell phones, etc. You might be able to mount the Airport Extreme behind your desk or to a nearby wall behind your desk to get it out of the way and reduce the need to stack things.