How common are missile defense systems on civil airplanes?
It's far from being common. The following carriers use missile defense on all or part of their fleet:


El Al
Israir and Arkia "can be assumed" to use the laser-type from Elbit (flightglobal.com, 2009).



  While Elbit has not identified any of the carriers likely to receive the equipment, a source familiar with the agreement says "it can be assumed" that all three major Israeli airlines - El Al, Israir and Arkia - are in line to be fitted.



FedEx uses Northrop Grumman Guardian (Wikipedia).


Missile defense systems are also reportedly installed on some VIP business jets.



Further reading:


Flight Guard
Directional Infrared Counter Measures
Civil Aircraft Missile Protection System


Related: How does the Guardian counter-MANPADS system work?