From my experience, it's probably your shoes. I've been using a standing desk for about a year and can definitely notice a difference in my feet dy to day depending on the shoes I'm wearing (personally, I find five fingers the most comfortable for me, but I think that's because I move around the most while wearing them). I did notice that adding a mat (currently it's just some really thick shelf lining, although I've thought about getting one of the restaurant style floor mats) made all shoes feel better. The shelf liner costs ~$5 so it's worth giving it a shot. Mixing in some sitting breaks as well (~30 minutes a few times a day) can also make a big difference since it gives your feet some time to rest.

1) bar stool for when you just gotta

2) a brick. A brick sculptor friend of mine was advised by a worker at the brick plant to keep one foot on a brick to rest it, alternating as needed. Says she's never had another day of back or foot pain.

Look into a standing floor mat like this: http://www.amazon.com/Sublime-Imprint-Anti-Fatigue-Comfort-N...

In another thread here, a few other members suggested the only thing that puts an end to this pain is compression socks.

http://www.amazon.com/s/ref=nb_sb_noss?url=search-alias%3Dap...