Question
Lately...when I've been sitting at my computer for a couple of hours my hips will start to hurt (one side at a time...never both together).  I have added pillows and foam to the seat of my chair and even purchased an inflatable donut (usually for hemorrhoid sufferers) but nothing seems to help.  Could this be something other than me needing to buy a new chair with better padding on the seat?

Answer
Without an actual hands exam, it is a little hard to diagnose.  But, sitting for extended periods of time affects the Psoas and Iliacus muscles, making them resistant to stretch back out when you stand.  A good stretch for them can be found here:  http://www.somatics.com/psoas.htm
I would try this first to see if it relieves what you are feeling.  If not, an examination by a good chiropractor to assess whether it is strictly musculoskeletal, or if referral is needed.  A good rehabilitation exercise program would also be warranted.