Many camera manufacturers have different opinions on the advantages and disadvantages of the two systems.
In camera sensor shift has the advantage of always being there, no matter what lens you should decide to put on the camera, and is thus its main advantage. However it is not viewable through the view finder, a problem that one might find quite irritating.
The advantage with lens shifting systems (such is IS or VR as called by Canon and Nikon respectively) is that they can be viewed through the view finder, something that most photographers will agree is an important thing, and will value much in the same way they use the viewfinders depth of field button. The key disadvantage of lens shifting systems is that they tend to cost more to implicate, which is the key reason why manufacturers such as Sony (a more consumer orientated manufacturer) have chosen to use inbuilt image stabilisation into the camera body.
As for the effectiveness of the two systems, there is very little difference, all image stabilisers remove around 2-4 stops of shake at relatively similar quality. If I were to make a choice, I would go with lens shifting, as it rely on the lens and I find it quite important to see the effect the stabilisation has on my subject as I am a wild life photographer often shooting at around 600mm.
However this opinion did not affect the choice of camera I went for, it just happened to work out that way. When choosing a camera there are much more important things to consider, such as upgrades (what camera will you by next) and lens, and customer support, and above all the way the camera fits your hand. Image stabilisation should be near the bottom of your list with gadgets such as sensor cleaning and Live view.