After mousing aggravated some of my shoulder problems, I switched to using keyboards with mice in them. I've tried a few, but the Adesso Tru Pro has been the best so far. I received it today: it has the slight elevation/separation between two hands, soft keys, and a nice track pad. It is a little big, but I kind of like that.
Previously I was using the Keytronic trackball keyboard, which was okay but not very ergonomic. The trackball also often got stuck, which was annoying. The keys are also pretty loud. I have also used the Lenovo Ultranav, which is basically the Lenovo laptop keyboard with both a touchpad and a ball mouse. I got the version without the number pad on the side so the mouse is in the middle. I found it to be okay but not sufficiently substantial: my hands get kind of funny after typing on it for a while; it might be because it's a mini keyboard.
If you are having shoulder problems with your mousing shoulder, you might want to try switching to a keyboard with a built-in mouse. I also type with my keyboard in my lap, elevated by a Lapinator so that my elbows can be at 90 degrees.
Worried about switching keyboards because you already have a fancy schmancy one you don't want to give up? My friend who was having mousing problems got this touch pad to use with his Kinesis.
Life lessons: computers are pretty bad for you, but the internet is so cool.