There are a lot of articles about if or when you should shoot in manual mode. I would like to settle this issue once and for all with the following guide lines.
If you own a regular DSLR camera you should be shooting in either aperture priority mode or shutter priority mode. If depth of field is important, shoot in aperture priority mode. If freezing the action or blurring the action is important, shoot in shutter priority mode. If you own a camera that is always in live mode like the sony a77 or a99 you could be always shooting in full manual mode unless you have to be extremely quick taking a shot. In that case the earlier mentioned strategies apply.
Full automatic mode rarely gives you what you really want, however if you are shooting RAW you will have lots of leverage to correct your images to your liking later. It's always best however to get as close as possible to the result you want in camera instead of in post.