I was seeing a physical therapist regarding problems I was having with my knees (chondromalacia, where the knee cap starts rubbing against the other bone), and she was actually the one who originally recommended I see a podiatrist because she thought my feet were causing my knees and even my hips to be out of line. The shoes mine recommended weren't too bad. Brooks Ariel -- even comes with a Disney name! I got them because I "overpronate" -- put too much weight on the outside of my feet. Check your shoes and if they're overly worn in one area, like the outside, that may be your problem.
http://www.amazon.com/Brooks-Womens-Motion-Control-Running/dp/B00AOQ0P00/ref=sr_1_1?s=shoes&ie=UTF8&qid=1405095338&sr=1-1&keywords=brooks+ariel But as someone else said, you can wear the orthotics in just about any shoe. Though probably not high heels. They're pricey -- like about $600 for a pair, but mine were covered 100% by my insurance.