We all know that autofocus is very convenient for everyday shooting, especially on cameras with tiny viewfinders that make manual focus difficult (like my Nikon d3000).
However, just like the exposure settings, there's a reason that dSLRs offer a manual focus option: sometimes the brain behind the camera makes better decisions than the "brain" inside the camera.
What are some situations where it's usually better to switch off autofocus and do it by eye?
Edit:
I was browsing through DPS today and found this article: When is Manual Focus Better than Auto Focus? It seemed relevant.