Have a clean desk is my #1. I work in a corner office with 4 windows, 2 in front of me and 2 to my right side, I do believe seeing outside has helped a lot compared to my last job where I had one window behind me. I also setup my whiteboard away from my desk so it causes me to get up. Keep all blinking lights (printers, routers, external HDDs, etc) hidden behind or beneath something. Other than that it's just good headphones and having lots of music.
get natural light, get fresh air, get quietness.
Not productivity related, but the most important thing IMO that an office should have is a view of the outside. It is more than just something nice to look at. If you spend as much time as I do in front of your monitor(s) you need to regularly focus on something in the middle to far distance to reduce eye-strain. I've done a quick search on the internets to find this: http://www.pasadenaeye.com/faq/faq08/faq08_text.html
I've no idea if this is scientifically proven or anything, but looking away from the monitor every once in a while can't be bad for you.