I have been avoiding using knee pads in Iaido because the ones I have always bunch up behind my knee and feel as though they are cutting off the circulation in my leg. I have the knee protector that came with the Iaido package A from Tozando.
Nike makes a softball kneepad that several people in my Iai dojo use when we're on hardwood. (Clicky)
I've used their volleyball thin-fit kneepad and like how thin it gets when compressed. It still bunches up a bit behind the knee however. Our Iai class is held in an Aikido dojo though so we have a padded floor and I almost never wear kneepads, they drive me nuts.
Out of curiosity, what kind of knee pain are you experiencing? Kneepads really only help minimize bruising on the outside of the knee (at least in an activity like Iai), if you're feeling pain in the knee, you may have something else going on.