I've used a traditional mouse and keyboard since I was around 7 and can easily spend a whole day in front of my computer.
Lately I've been wondering if it's simply just my inability to sit still which has helped me so far. I feel like I always need to change my sitting position. I can sink down in my chair, put my legs up on something, move my feet, lean on my desk in awkward positions, stretch and twist my body and so on. Not because anything hurts, but because I just feel restless.
But sometimes when I've been intensely in the zone while programming, I don't move as much and then I might start to feel some stiffness in my arms, fingers, etc. I would also notice my eyes get sore, maybe because I don't blink as much?