Oh, I can talk your ear off about Vibram Five-Fingers. It's been a while since I've more or less quit running (I keep meaning to start up again. I'm bailing on this year's marathon.
), but I ran in them exclusively for about...six months to a year, and it made a huge, huge, POSITIVE difference. My knees stopped hurting, first of all, and my calves got a LOT stronger.
It takes a while to develop your feet strength and to learn with correct form, but it really changes everything about the way you run, when you stop relying on your shoes' cushioning. That actually does a lot more harm, because it encourages you to land heel-first, which sends the shock right up from your feet to your knee when you hit the ground. When you run without support, you are forced to adopt a forefoot-landing style, a lot more like a sprinter, and you start to use your foot's architecture to absorb the shock instead, and then use your ligaments to spring your step forward.
Running in boots? Ugh, I can't even imagine doing it again. I did that once, and screwed up my lower back.