I dealt with the same pain after pushing hills late last season, I wanted to go into the winter strong.... I spin up hills but I did stand for some very steep sections. I soon had the pain at the bottom of the knee cap at the point of attachment as well. My issues were intermittent, i.e. the pain would be there one day and not the next - never during the ride, long story short - it developed into patellar tendonitis, a real beatch! As others have stated, have your fit checked and lay off hills and big gears if you are hurting on a semi-regular basis. Also, ice the knee after hard hill rides, this helps to quiet inflamed tendons and could have helped to forestall my problems. I am just relaying my experiences so others do not make the same mistake I did. Make sure your pain is muscular not tendons.
Good luck and be careful, I'm in week 6 off the bike and I do not know when I'll be able to get back on.
A good guide to knee pain:
www.cptips.com/knee.htm