I have it too, with weak ankles and flat feet! Doh!

I have super arch support in all my shoes, and I do foot stretching exercises at night. I'm not sure if that helps or not, but it makes it feel better to me, so I do it. I also have a few foot odds and ends that I bought from footsmart (online store).
I love Birkenstock shoes also, I fondly remember my first pair. The relief, the pleasant feeling as I walked... the jibes as I walked through the door at home. Yes, actually, I was a pseudo-hippy, and I went to Santa Cruz to prove it!
In addition to my super-support athletic shoes I work out in, I also wear MBT's. They're expensive ($120+), but I really like them. I'm slowly breaking them in -- they give a rolling motion while you walk that seems to help me. Plus, they're supposed to help cellulite, so you can't beat that! (I'll believe it when I see it)
For workout, I do the elliptical most days, and the treadmill only once a week. If I do walking/running more than that, my feet are like walking on glass for days. The elliptical doesn't hurt my feet or my knees, and I can do it for an hour. I like having my breath and body be the ones to give out, instead of quitting for the pain in my feet!
My doctor told me to just do what feels right (big help he was!), and to make sure I have support. I'd love to do swimming, but the beach is my only access right now... and you won't see me there in a bathing suit yet! The operative word is Yet.
