Thanks madcow.
When I posted I had just gotten back from the gym. Id taken 20 mins to warm-up and stretch my back, hips and legs. I'd squatted bodyweight 20 times, heels close toes almost straight; 95lbs x 10, 135 x 6 (hurt knees), lots of stretching, 185 x 6 hurt knees, 225 x 11 - terminated set (was going for 30 and my muscles were feeling great) knees were getting more unbareable with each rep.
I'd had some problems with my left knee. Some patellar tendonitis and instability that I had sorted out. The last few weeks both knees have started to flare up again. I think it's just overuse causing tendonitis again. I'll probably just leave them for a few weeks. It's tough because I stress my knees doing:
Push Press, Deadlift, squat, Bent Barbell Rows
Thants half of my routine!