There are several great workouts you can do at home to workout legs. Now, keep in mind, running is not so much about building leg muscle, but a more cardio related activity. I'm not saying you won't work the muscles, but most people don't run to build leg muscle.
Now, on to leg workouts. There are plenty of good body weight leg workouts out there and generally (in my experience) I've only ever had knee pain from weighted leg workouts (besides running). I'll keep that in mind when I recommend workouts though.
Squats are a great exercise for working legs. Keep in mind, they do sometimes cause knee problems, so if you start feeling pain STOP. Squats will work the quads.
Lunges are another great leg exercise. They work glutes and hamstrings. Again, keep in mind, these may cause knee pain, but generally only with weight. STOP if you feel pain.
A good stationary workout (that shouldn't cause any knee pain) would be wall sits. These are definitely not easy and will work quads.
Click here for many more good leg workouts.
Everyone is different when it comes to injuries. Some of these exercises may give you pain in your knees, while it may not for other people. The safest way to avoid injury is always maintain good form and if you feel any joint pain STOP what you are doing.