Nikon D5000 - it's about 5 years old now and bought new. I've changed lenses, zoomed, un-zoomed, tried auto focus, tried manual focus, varied the aperture, checked that the speed is high enough to avoid shake, switched on the anti-vibration thing, switched it off again.
I've fiddled with several aspects of focus priority and tried it all in several modes A, M, P & S.
I've locked up the mirror and given the innards a good inspection and checked if the mirror is seating OK.
I've even taken to writing notes about each image and comparing notes with what I can see. All in all I've played with it for maybe 5 or 6 hours and I know the focus section of the manual by heart.
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Nikon SLR not focussing properly 
Nikon SLR not focussing properly 