I have used Hugin quite a bit (but by no means an expert), and it does all 4 steps quite well, normally. (if any of the exposures is WAY different in light level, you might want to use GIMP on that one to bring it closer to the others.) Once it Aligns the photos, you can move the conglomeration around to straighten it, try a different projection, and then crop to what looks good.
If things don't align as well as you like, you can add control points. I have even thrown it four photos that were actually a vertical panorama, and it figured it out and aligned perfectly on its own...

There are four steps, whichever program you use: (1) combine all the images into one big image, e.g.one per layer (File- ->open as layers in gimp)
(2) correct for rotation and make obvious exposure corrections to the photos - this is especially necessary if the lighting, focus, or camera settings such as exposure time and aperture varied between shots at all;
(3) determine known common points in each pair of pictures and move them to connect at these points, using perspective and barrel distort as needed
(4) correct colour casts, darkness etc between separate parts of the joined-up image and crop away the uneven edges.

Hugin will do step 3, which is the hardest part. The others, you can do in gimp.

Liam (slave ankh)