I ditched padded BS a long time ago. All my knee problems came from running in Brooks Beasts and other cushioned monstrosities. When I used to run, I'd run in these European minimalist shoes I spent a big penny on. They're black slip ons and they work for any use. I still own them and they're just as comfortable as when I purchased them.
I also have a pair of Vibrams that I'd occasionally run in, but the pair I have has hard plastic on the front that dicks into the front of my toes, so despite them being comfortable in all other aspects, the toe-digging makes them unbearable to run in after a couple of miles.
I haven't run since last summer, but decided I wanted a new pair of shoes for lifting and walking that aren't slipons, so I went to the Nike Store in search of Nike Free 3.0s. It was the only store in my city that I could find them in, but they didn't have my size so I settled for the 4.0s. They're very comfortable.
What about you guys?