I get cramps in my thumbs from time to time, other fingers and my hands, too.
My mother-in-law had to have surgery for her thumbs...
http://my.clevelandclinic.org/disorders/trigger_finger/or_overview.aspx
An article that deals with some of the trouble one can have with fingers.
I am not sure I can help a whole lot but I get this all the time, one hand or another. Doesn't really make a difference which side sometimes.
It usually happens to me also when I type a lot or use my fingers for lots of repetitive action. I've had it checked out from my doc and it is not carpel tunnel syndrom. He said it was just the stress of doing this kind of work. His suggestion was to take breaks more often and do stretches of you fingers and hands.
Usually issues of the hands and arms when typing a lot is due to not moving the arms and hands from that situation enough.
Try moving your hands away from the keyboard when you are not actually typing. So when you are thinking of what to write or something like that just let them hang for a second or two. Stretch your fingers out or put your hands together open faced and stretch for a while. Make sure to move you wrists around too. Hope that helps.