Cornell University has weighed in on the standing vs. sitting at work debate. Their conclusion is that while standing is arguably better than sitting in terms of calories burned, standing alone isn't sufficient - actually moving about is required.
In my experience over several months of working at a standing desk, all their points ring true. Fine motor control (typing) definitely took a hit for awhile, and standing was definitely more tiring at first. But my typing while standing is nearly as fast now as it is when I'm sitting, and after the first week my feet stopped bothering me. One thing I think the Cornell study missed is that I am much more likely to move around - both in terms of shifting my feet and weight, and in walking down the hall to the printer or co-worker's office - than I was when I sat while I worked.
On a personal level, I've noticed a huge improvement in my posture since I started standing. I actually get uncomfortable when I slouch on the couch now.
Standing at work is not a silver bullet, and I've taken a LOT of crap from my co-workers for my crazy computer set-up, but it's accomplishing what I wanted it to: improving my posture and keeping me more alert at work.
Related: Standing Desk Part I