Get a good podiatrist and check into orthotics. Shoes are incredibly important (I personally wear very nice athletic shoes in a lab environment or hiking boots in the field). If you spend hours on your feet high fashion goes out the window and practicality comes in. The Easy Spirit shoes are often comfortable but it depends on your foot's features. Mine is very narrow and hard to fit so my options are limited.
You didn't say what you were going to do exactly but I assumed you'll need to look a lot nicer than I do since I wear a lab coat over clothes and when I don't I'm sure to ruin something with a chemical splash.