I noticed yesterday while I was playing some 1v1's that by the end of my games (~15-30 minutes long) my hands were really cold. At first I blamed it on my pathetic excuse for a heating/cooling system in my apartment, but after thinking about it I realized there's no way my air conditioner can be evil enough to only get cold while I'm trying to keep my apm up.
A fellow clanner suggested it could be poor circulation. I'd heard about this in the past, but couldn't recall having similar issues in the past. I then looked down at my desk. Something seemed odd. What was so peculiar about it? I realized I have my keyboard pushed all the way back on the surface of my desk. Over a few years I've developed the habit of pushing everything on my desk backwards, including the mouse and flat panel monitor as well. Resting my arms on the desk feels much more comfortable than having to levitate them in the air.
But then it hit me. My arms were resting on the table, except when I simulated playing StarCraft I noticed I seemed to be using the edge of the table as a pivot for my arms. When I moved my left hand from the 'a' key over to the region used for '0p9p8p' one part of my arm remained in contact with the edge of the desk. I noticed it was similar with my right hand on the mouse as well. Apparently, during games I would keep my arms in these positions for extended periods of time and was cutting off some of the blood circulation to my hands. I knew it couldn't just be me getting 'cold' since I tend to feel hot rather than cold.
The solution was simple: just get used to having the keyboard and mouse close to the front of the desk. I still am trying to decide which position I am most comfortable with, but just by being wary of what I was doing before, I haven't had any more problems with cold hands.