Update – Not GIMP, but an excellent tutorial written by Pat David on using open source tools (Enfuse and Hugin image align) on Windows to focus stack! http://blog.patdavid.net/2013/01/focus-stacking-macro-photos-enfuse.html
A quick video on YouTube to get you started with focus stacking in Gimp. If you are new to focus stacking, it is a method by which you can increase your DOF by taking multiple exposures, each focused on the “next” section of the image (front to back), and combine them into one “in-focus” photo. Works wonders for macro photography.
A GIMP plugin for image alignment. http://registry.gimp.org/node/24248
The video is not bad, but what you are really doing is blending two or more layers into one via masks. Similar to this technique. http://gimpedtutorials.com/index.php/blending-photos/
And similar to this HDR technique: http://www.gimp.org/tutorials/Blending_Exposures/
Also – some free software to combine the images – http://hadleyweb.pwp.blueyonder.co.uk/CZM/News.htm