Physical therapist here (but not your PT obviously), you are practically asking for medical advise and this is probably the reason you are being downvoted (against the rules of this sub). This is a question you should be addressing with your PT and not over the internet to someone random, as this could be a risky move and can also hinder your progress in PT. Don't hesitate to ask specific questions to your PT, as they are trained to answer these types of questions.
Looking at your situation:
Large lifts that require a ROM of more than 90 degrees. Squats (my heart aches), deadlifts, etc. i.e. exercises that require a large ROM of the knee joint, even if it's performed as a closed-chain exercise
Machines that don't allow full support of the foot (as in my feet aren't flat on the ground). I.e. hamstring curls, quad extensions, etc. This practically means no open-chain(http://en.wikipedia.org/wiki/Open_kinetic_chain_exercises) exercises
Machines that place direct pressure on the knees. Prime culprit is the adductor/abductor machine, where the pad rests against the knees. No direct pressure on the knee, at least no pressure from the sides of the knee. This does not clarify whether you are allowed to place pressure from the front of your knees like when you are doing glute-ham raises, as another commenter has posted
Wall squats & wall sits. Not allowing my joint to go beyond 90 degrees (aka "parallel"). For additional weight on the squats, I can just hold dumbbells or plates by my sides. Wall squats perhaps to reduce the stress being applied to the knee, wall sit is an isometric exercise so it applies no shear force to the knee. I would guess you are to use the dumbbells with the wall sits and not the wall squat, otherwise it wouldn't make sense to prescribe wall squats in the first place. You might want this clarified
Leg extensions via the cable machine. I LOVE these. Done on the giant set of machines with height-adjustable cables in the middle, I just drop it down to the floor and attach to my ankle. Back, Front, Side, and diagonally back are usually the four directions I do. These are technically hip exercises, just that you have to isometrically use your quads/hamstrings to prevent your knee from bending while performing. Once again, it is isometric so it prevents the shear force being applied to the knee
Keep in mind that these are just my interpretations based on your post, as you can see it isn't even clear enough for another PT to understand. Although I posted my interpretations, I advise you not to stick to my words or to other people in this thread, but to clarify with your PT for your own safety. Good luck with your recovery.