Hello,
There is a downloadable program @ Cnet.com -free
http://download.cnet.com/MedHelp-s-P...-11009361.html

and a free online pain diary here- (also a paid version if you want that)
http://www.reliefinsite.com/

there might be other programs & websites if you do a deeper search.

Or you can use the Fibromyalgia and Chronic Fatigue forum and journal your pain /symptoms on a thread there.
http://neurotalk.psychcentral.com/forum12.html