Jessica, my physical therapist had me doing unweighted ball squats as baffled mentioned, just going down until you start to have pain, hold for a bit, repeat. I managed to do enough over the weekend to have lots of delayed pain for a couple days (as mentioned on the chat thread
). He also had me do lunges, just carefully placing my feet and again lowering only until I felt any pain, then raise up. No walking lunges, no weight.
The other thing he had me doing - and this depends on why your knees hurt, I think (Mine is the malalignment of my patellas) - is hip strengthening exercises including leg lifts in various guises. Also hamstring and quad strengthening including leg extensions (using the cable machine) and leg presses.