I don't run barefoot (tried, bad idea), but I run in flat shoes, like kung-fu slippers.
I think it's much better to run like that than in running shoes, you are forced to watch how you run, you learn not to land on your heel, but rather to use your front feet & toes to absorb the impact.
My knees are fucked and runing flat helps.
https://www.youtube.com/watch?v=b-iGZPtWXzE