I believe autofocus is more accurate than manual focus, especially for digital cameras. On digital cameras, you only have either LCD or a visual indicator in the viewfinder to tell that you are in focus. Of course, there are some photographers that changed their viewfinder screen to include a split prism design that aid in manual focus. But under normal circumstances you can always rely on the electronics to perform much better than your eyes.
There are some instances where manual focus comes useful. Dark scenes make most AF hunt due to lack of contrast. With your eyes a better equipment in low light areas, manual focus gives you more consistent and better gauge of something in focus. AF can also be confused in situation when you have some faint objects in the way which infuse the electronics of not knowing which object is intended to be in focus, such as branches, leaves, window grilles, or human profiles. Manual focus will be a good choice where you override. Of course, you can always try your luck and let the AF do it's job making guesses.