Found this article on the topic and it covers more than just the usual seat height for/aft position.
http://www.kvanproductions.com/cycling/knee_pain.htm

another excellent article Dan.

Good article. As someone who has had to deal with knee pain off and on for a while now due to my aging ACL reconstruction (17 years post operative in December) I can say I've carefully tried to follow all the points in this article with pretty good results. I'm going to put in my pitch now for my Speedplay pedals. Anyone who has chronic knee pain really needs to think about these, especially roadies (I've never tried the Frogs for mountain bikes). Thirty degrees of radial motion lets your feet (and hence your legs and knees) settle in to a natural position. They feel a little weird at first if you're used to Shimano or Look systems, but I bet once you get used to them you'll never go back. Just food or thought.