Hmm. Mice and keyboards do far more damage to me than any controller ever did, and I've owned a good number of the well-known consoles. It's interesting how even something like this can be subjective.
I've been meaning to get a controller (probably another PS3 one) to use on PC. I still have a USB adapter that I used to use with an SNES controller.
Yes, mice can be bad too. I remember I had to stop playing Torchlight II, just too much damn mouse clicking. Also, I spend a fair bit of time on a computer doing graphic design, but I alternate using a Wacom. Using different interfaces is the key to avoiding repetitive stress.
I do miss comfy couch gaming though