Joint issues can affect a lot of people, for several different reasons. Certain workouts may actually make your joint pain worse. Before I had started working out, walking -- especially uphill caused some knee pain. Also, workouts like jogging on concrete gave me some discomfort, as well.
There are definitely other exercises you can do that will burn calories, build strength, reverse joint issues -- without the grueling pain.
The Arc Trainer
This sort of looks like the elliptical, but the movement is a bit different. For the arch trainer, it has more of a gliding motion. Also, the movements are more flexible. You may adjust the machine so you can have a short range of motion, or be able to have a greater range of motion. You can also mimic high-knees (or climb) on this machine. Again, it's low impact, so it should not have an impact on your joints. It has also been argued that the arc trainer burns more calories than the elliptical! Give it a try! I think you'll fall in love with it.
I personally had never been a fan of cardio, mostly because a of the high impact and much it hurt the way it shouldn't -- but when I hopped onto the arc trainer, I discovered that I can love cardio in different ways. I've felt like I had more of of a productive workout with the arc trainer, than a consistent-pace jog or even from using the elliptical machine.