I have a similar problem with flat feet and occasional episodes of plantar fascitis.

I used to use the Sorbothane Graphite Arch years ago, before I got custom orthotics:
http://www.roadrunnersports.com/rrs/products/SOU28/

I didn't like my first pair of custom orthotics for my running shoes. They were the half-sole, hard thick plastic kind and my feet never quite fit in my shoes properly.

My current orthotics are similar to the Graphite Arch in that they have a thin layer of plastic shaped for my foot (from heel to ball of foot), but they are lined on top with squishy Spenco-like stuff that is full foot length.

My podiatrist also made me an extra pair of orthotics that is thinner profile and fits inside my dress shoes. I was miserable in dress shoes before I had these!

If you can't find an over-the-counter option that works for you, I highly recommend getting custom orthotics.