Trying to shoot a complete spherical panorama, I found that no software was able to stitch correctly the nadir images I had. PTGui Pro 9.1 and Autopano Giga came close but no cigar as they say. I found a vague mention that says is is possible in an answer to this question which says:
There is of course a way to shoot nadir and zenith with a tripod to eliminate it from the picture but believe me it is extremely complicated and involves moving the whole tripod several times.
This brings me back to my question:
How to shoot a Nadir image for a spherical panorama with a rectilinear lens?
For one, I do not have a fisheye lens. Plus, this severely limits the resolution of resulting panoramas, so I really want a solution that works with any rectilinear lens, although most importantly between 12 and 55mm on an APS-C sensor or 16 and 75 on a full-frame, since those are the most common focal-lengths I have with cameras of the respective sensor sizes.