I'm always surprised to see guys set up improvised standing desks on filing cabinets and stuff like that. From several years of experience: You need to be able to sit OR stand at your desk. In a very short time, you will automatically alternate between these positions whenever you feel tired in the back (from sitting) or feet (from standing).
I would never work somewhere that didn't provide a motorized desk. I have gotten so used to it that I even have one in my home office (http://imgur.com/A1eS2), set me back about a thousand bucks, an amount most of us would spend on gadgets without blinking.
I had a habit of going for a mid-day mile or two walk to help balance things out, but the weather has been so toasty lately that I just can not bring myself to do that anymore.
I am definitely feeling the effects of the sedentary lifestyle.
My standing desk is just a normal desk put on top of cinder blocks so my drawers and surface are all setup for standing.
Both of those cut down on the time I could handle standing.
It's important to ergonomically adjust your desk so that it's in the correct position, of course. Stand normally with your arms limp at your sides. Now, without moving your elbows, bring your hands up such that your forearms are horizontal, hands straight in front of you. Your hands now indicate where your keyboard should be -- roughly an inch or two below your elbow. Your mouse should also be reachable from that position without moving your elbow.