Auto Focus systems of modern cameras works nearly perfect, but still there are some situations that you can take better results by using manual focus. Such as;

• If you are photographing something in a dark environment, where the light amount is so low, your camera may not be able to find a light-enough point to focus on. In these kind of situation you have to focus manually to the point that you want. You may face with this problem while you are shooting nature pictures in the wilderness where there is no light source but the moon at nights.
• Also your camera can focus on nearer objects or points than you want, when you are shooting through fences, branches, nets or glass. Auto focus systems of cameras tend to focus foreground objects, so if you are shooting a landscape between branches of a tree, your camera’s auto-focus probably will focus on the branches not to the real subject, or scene you want. In this case you should switch your camera to the manuel focus mode and focus your subject manually.
• Macro, is a kind of photography that you have to work with a narrow depth of field that means a small part of the object will be sharp and clear and the rest of the object will be flu (blury). So you must decide which point will be the focus point in order to draw the attention of your viewers to the right spot. as a result using manual focus at macro photography is a good choice.
• When taking portraits, to avoid your camera focus on undesired parts of the face such as nose, you can focus on eyes manually. (of course if you want to focus on somewhere different than eyes it is your chocie, i just gave an example)