I think monitor arms are a must. Looking straight ahead rather than slightly down makes all the difference to me. And 2 computer monitors minimum, three if you don't have an external video screen (TV, projector).
I have a Command 8 for home and use a D-Command at work. If I had waited, I'd probably have gotten the MC Command as opposed to the Command 8, just for it's ability to program macros and expandability. The D-Command is great with it's ability to dive into plug-ins, and have pretty much any control at my fingertips. On my most recent show I abandoned the mouse (almost unplugged it) just to see if I could get by without it. Not only was I faster using keyboard shortcuts and the control surface, but that annoying pain in my right shoulder decreased significantly!
While I am looking at getting a new chair in the next month (at the recommendation of my chiropractor) my favorite ergonomic tool has been a stability ball. You simply can't slouch. I only bring it out once or twice a week, just to kinda readjust. But after a long day at the console, it's great for a stretch. And an added bonus, it has a nice deep ring to it when bounced off walls.
Just stumbled across this workspace planner. Enter your height and it'll spit out the correct heights and distances for your chair, keyboard, & screens whether sitting or standing.