One bit of information that I have discovered in my own experience is that a softer mat is actually more damaging to knees than a mat more firm.
Let me just back up Mark's observation (which would have seemed strange to me a year ago) with the experience of one of my kohai, whose knees are fine on rice straw mats, but suffer when we practice on mats made of insulating foam. He says it has something to do with the way the foam conforms to the contours of his knee; it seems to exert greater pressure, at least for him. Just this week his knee gave out and he's been unable to do suwariwaza for the last few days. Any idea why a soft mat can cause more damage?