The Minkowski Portal Refinement method, also known as XenoCollide was developed by Gary Snethen (Xeno). As far as I know the original implementation in 3D is only described in Game Programming Gems 7 where working source code was also provided.
As of this writing these are the main implementations that I found online:
Library for collision detection between two convex shapes
Jitter physics is a realtime physics engine for .Net
A 2D Implementation of the Minkowski Portal Refinement (MPR) Algorithm
A demonstration of the Minkowski Portal Refinement algorithm written in Ruby