I went from using an optical trackball, which was doing my thumb in (pains all up the arm into the shoulder), to an "old fashioned" clicking mouse, but on a mat with built in wrist support. This has helped a great deal although prolonged use can still cause problems.

Getting the heights of desk / chair / screen combination right for you can also help. Standard furniture is made for average people and if you're tall / short / small / large in any dimension, the dimensions won't be right for you.
Get a GOOD chair which is plenty adjustable. Once the back is supported adequately, other adjustments can be made.

Good luck
Paws