As a photographer I'm 'camera agnostic' and use both Canon and a Nikon systems on a daily basis, so I do have real-world experience with both systems. Both the Canon and Nikon stabilization systems are designed to perform the same function (stabilize the image from hand-held camera shake), and they do it in the same way (a floating element within a lens manipulated electromagnetically). In my experience, there is no appreciable difference between the two systems.
To address your additional question, Thom Hogan's 'rules' as outlined in the the cited article will apply equally well to Canon's IS system and are more-or-less what I teach my students about image stabilization (though some of my students would probably say that Thom's article is more succinct than some of my rambling explanations!).
Bottom line: Don't make IS or VR the 'deciding factor' if you're in the process of 'going Canon' or 'going Nikon,' for all intents and purposes the systems are equivalent in functionality, features, and operation.