Originally posted by Jonathan Mac - Be systematic with the shots.
- Don't skimp on the overlap - more overlap is good. It means more shots but reduced chances of missing a bit.
- Be generous with the overall field of view - go far beyond what you hope will be the field of view of the finished photo.
I think that third part might be the most important- after doing any sort of distortion corrections you're going to end up cropping a lot of misaligned stuff around the margins, so overshooting the framing is the safest way to do it.