I have problems with my knees (petello femoral syndrome) as well so my dr. gave me a handout full of exercises to add to my routine. My knees felt good even after doing them and I could feel a burn in the leg area and even up to the rear in some of them. Some of the more common stomach & butt toners I had to change up a little bit to make it easier on an old back injury and my knees.
I do crunches instead of sit ups but I put my lower legs up on a chair or couch. It still give you a good tone for the stomach but has a lot less impact on your lower back. I also do the knee touches to my elbows but I do it as a quick alternating to each knee while laying on my back on the floor. Then there are leg raises. You lay on your back and keep your legs raised approximately 8 inches off the floor for 10 seconds. It is really hard to do but it helps toning those areas as well. I also do an overhead reach with my stomach musles tightened and that helps with the stomach. Walking, as always, is a good low impact toner for the lower half of the body. I find if I try to keep my stomach muscles tight as much as I can throughout my entire routine, just about any of my exercises can help with my stomach.
It's been a while since I've been able to do my routine due to surgery on my toes so I'm drawing a bit of a blank on the knee exercises cuz a lot of them help strengthen the muscles around the knees and I even feel a little bit of a burn in the rear area. I also feel as though I am forgetting a few of the stomach toner exercises that I do.
I also find the "3 hour diet" to be the most effective diet for me. All it really is is eating smaller meals every 3 hours. You can still eat anything you want (I have spurts where I eat a lot of chocolate and have still lost weight) just smaller portions. You generally start an hour after you get up with breakfast and eat every 3 hours after that until an hour before bed. I have done great on it even though I have been unable to do my exercises for a few months now. I have either maintained the weight loss I had experienced or continued to loose weight. Admittedly, being a woman, I did have some points where my weight went back up by a little bit but would go back down within a week or two (never more than 5 pounds that I would shed after my female issue had completed it's course).