I go manual focus, and aperture. If you're familiar with photo fundamentals, you will always be better off being in charge of the technical parameters of an image. The only time I use auto is with small point and shoot cameras and smaller, automated video cameras. On the video cameras, the lens just goes around, there are no distance markers or infinity, or stops marked, so working with it in manual is a study in frustration.
But if you're working with an slr or a good 3chip video camera, you will have excellent manual controls, so use them. If you don't know how, learn, and buy a camera which offers good control.
Best,
John