I noticed that some of my lenses auto-focus more accurately then others. (Assume perfect light conditions and fast shutter speed) Zooming-in on say the center focus point (if only the center focus point has been used) sometimes reveals that the lens overshoot or undershoot the focus just ever so slightly. I also almost always get a better and sharper image when focusing manually (and breathing correctly). I mean the autofocus is not bad (seems best on my prime 50mm lens, less perfect on my 70-200mm telephoto) but not perfect.
I might now be thinking this up as I write along but If I remember correctly I've read somewhere that the Canon 50D body has some kind of an feature that can fine tune the AF for differently for different lenses.
In the end I decided to go with the Canon 60D body. My question is: Is it possible to somehow calibrate the auto-focus with my body to perform more accurately?