We've been recommending that people use one of two panorama stitchers for some time now, PTGui and AutoPano Pro. 

AutoPano Pro works great if you shoot with a very wide-angle or fisheye lens, but if you're shooting with a 10-shot or 12-shot rotator head, sometimes AutoPano (or for that matter, most stitchers) have trouble stitching some images. This is really common if you're shooting a scene with large sections of solid-color wall or have the camera too close to the wall. With AutoPano when this happens, it can be really tough to fix these issues. We set out to find a solution and did publish a screencast on adding manual control points with AutoPano Pro.

In related news, PTGui has launched version 8.0, with many great improvements, including bug fixes, increased speed, and a much easier-to-use control point editor. I had pretty much given up on PTGui for stitching problem panoramas, especially after I had figured out the workflow in the above screencast with AutoPano. However, I just tried re-stitching a problem pano in PTGui 8 and the new control points editor made it MUCH easier. Also, a lot of annoying bugs have been fixed. So I will be giving the new PTGui another fresh look and consider recommending it again to customers.