Obviously, everyone's knees are different and you don't always perform every jump or trick as planned. Therefore, you end up taking some landings out into the flats even when you don't plan to. I have two bad knees, one with a torn PCL and the other on the verge of tearing something. Bending my knees when I land definitely helps, but so does the board I ride.
I picked up a Shane this year and my landings have never been softer. Last night I took a spin on a LF Witness and the landings were noticably harder on my knees than my Shane. The first set of the night I rode my Shane and the second set I rode the Witness. Same boat, same wake, same rope length, same speed, and the same occasional landings in the flats. Bottom line for me was the Shane gave me pillow soft landings and the Witness did not.
You can do all of the things people are suggesting as they will help your knees, but a board that better suits you can definitely help as well.