I use an assortment of things from very expensive to free.
Autopano Pro is one of the best, especially for very complex stitches, lots of pictures or both vertical and horizontal within a single stitch. This shot is a stitchup of 33 frames (I forgot to pack a wide angle lens, so took many shots at 200mm+) and Autopano had no trouble putting them altogether.
I've also used Arcsoft Panoramamaker and it seems to do a reasonable job, even when Autopano struggles sometimes, though I've no idea why this is. As I remember it's limited to vertical OR horizontal though and you don't have that much control of the output image size (small, medium or large
).
Finally, panotools is free, but really needs a frontend, like PTGui to make the most of it. Even then, it's not so user friendly as the others I find.