Here are steps, that helped me:

1. ensure you don't have diabetic - very often one of the consequences of diabetics are problems with feet (so called "diabetic foot").

2. ensure you don't have neurological problems - caused by many factors (from side-effects of diabetics to low potasium level)

3. ensure you don't have any cardiac/veins problems (myself being overweighted [fat, lets call it straight] is have high blood pressure which can silently make tremendous damage to your body - even feet)

4. you HAVE TO take breaks from sitting! Stand up and take few steps every hour. This will cause better blood flow in your legs.

5. keep focus on your posture - probably most of the programmers and it workers tend to do work in half-laying position (which itself is not so bad to be clear), but if you correct your self once in a while and try to sit with your back straight - this will also improve overall health of your spine and blood circulating system.

6. Less coffeine, more water.

7. I personally have a condition were I constantly move my legs when sitting. Some of my friends are telling me I lullaby a devil on my knee. Some call it Restless Leg Syndrome. Whatever it is - my legs are for most part of the day in motion. But, I know that not everyone have this kind of feature build in themselves. Investigate things like under desk bikes or steppers. I even saw one time device which looked like some kind of underdesk swing for feet - you would place each foot on wobbly platform and through the day you would move them in every direction.

8. If above point is not for you (for whatever reason) search for rubber spiky pillows. They look like round pillow, with lots of little rubber connes. Often advertised as lower back stress relievers. Put one under the desk and keep your feet on it through the day - it will increase blood flow.

9. Keep your feet at comfy temperature. Some are heat-likers some are cold-likers. Whom ever you are - adjust how you keep your feet through the day. Either ware a comfy, fluffy socks or very thin one. Maybe slippers aren't a bad idea.

10. Take good care of hygene of your feet. And by that I don't only mean washing them. Also ensure you are fungus infection free, keep them soft by some cream of hot, salt water rinsing.

Finally - invest in the comfiest shoes You can afford. I cannot stress this enough. Bad shoes can do long lasting discomfort for your feet.

And thats it from me :)