I recently bought a Pixhawk flight controller with GPS module. The GPS module kit doesn't come with an antenna mounting system (though you can buy one separately). Thought I'd try to design something simple and replaceable myself.
This design consists of a tray for the GPS module (with a tight fit) with rubber-bound cleats and two mounting sockets (one to connect to the multi-rotor frame and the other to the GPS module tray). The top mounting socket is secured by the same rubber-band that keeps the GPS from flying out of the tray (which is topless). The bottom mounting socket can be trimmed and drilled to fit whatever you use for your multi-rotor's frame (its a solid 1mm thick plate - depending on your floor/ceiling print settings). The top and bottom mounting sockets have holes that will accomodate a standard bamboo BBQ skewer.
This is a work in progress - I've not tested the system yet and I don't know yet if it will transfer too much vibration to the GPS antenna or if it will slip causing the GPS antenna to become missaligned with the multi-rotor frame.

I printed this on a MarketBot Replicator 2 using Matterhackers Black filament at standard layer thickness (200um) at 120mm/s speed, 205 degrees C - directly on the acrylic build plate.

UPDATE:
Added a specific bracket for the AnyCopter hub from Flitetest.(http://store.flitetest.com/electrohub-plates-only/)

Also updated the hole diameter to better fit the BBQ Skewers I use without requiring any glue or sanding.

Print 1x 3D_Robotics_GPS_Module_Mount
Print 2x 3D Robotics GPS Module Mount Shaft Cleat

or if you are using the AnyCopter Electrohub

Print 1x 3D_Robotics_GPS_Module_Mount
Print 1x 3D Robotics GPS Module Mount Shaft Cleat
Print 1x Anycopter GPS Mount Bracket.