As mentioned in various ways above, I use MF when I have to...ie, when AF doesn't focus where I want it to.
Understanding the "way" the camera decides on what to autofocus on is critical, as is choosing the correct autofocus points the camera should use. For Canon users, AF will typically select the closest subject that falls within the selected (available) focus points. Most times, I select center point only as the autofocus point to use. That way I tell the camera what to focus on, rather than letting it choose from more than one possible points. Other times, especially when I want something not in the center of the frame focused on, I'll let the camera choose from 9 or more (5D3 has 61 AF points). Recognize that for moving subjects (people, cars, etc), the ability to keep focus lock is far better done by the camera than by a human.
As mentioned above, shooting through a fence would confuse the AF, as does trying to focus on someone in a crowd, not in the one of the available focus points, or, the camera simply focuses on the wrong person. Then it's time for MF. I sometimes use MF when shooting items I'm selling on
ebay when the AF just won't pick what I want to focus on. I also switch to Live View and focus from there, since I don't have any urgency to get "the shot".
Although I'm a former 35mm shooter and accustomed to manual focus, these days, I let the camera do the work 99% of the time.