A couple of people have already mentioned this but the height of your chair in relation to the desk is the main portion of your wrist pain, not the mouse or mousepad. When I use other peoples' desks and their chair is lower than mine, my wrists starts hurting pretty fast. At college my wrist was always in pain until I bought my computer chair that put me high enough so that my wrist isn't really at any sort of angle.
Another HUUUGE factor is if your chair has high armrests. When I sit in this chair and put my arm on the mouse, from my elbow to the end of my fingers is entirely horizontal. If you have to "hold" your arm up while using the mouse, then your wrist is gonna take a huge strain. Make sure the arms of your chair are elevated and support your entire arm.
It sounds stupid, but I've had a lot of experience with this shit because the slightest wrong angle and my wrists/shoulder start going crazy with pain. It's all in the armrests/chair/desk.
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"A Darwinian attacks his theory, seeking to find flaws. An ID believer defends his theory, seeking to conceal flaws." -Roger Ebert
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