I sometimes get an aching hand on a longish flight. I fly with my left hand and having tried all sorts of balancing acts with elbow on leg, hand on top of the yoke, on the side of the yoke etc have come to the conclusion that it is sometimes just better to swap hands every so often.
I do notice as well especially with the pa28 type throttle that shooting a few instrument approaches where your hand is always on the throttle leaves me with an aching right hand and arm.