The classic sissy squat puts the quads into a fully lengthened position and makes them scream all by their lonesome.
Now, someone with weak-sauce sprinkled all over his knees is going to complain about how sissy squats are bad for the knees. Wah. Have you taken any time to think about why they hurt?
It could be because your VMO is puny and can't tolerate the tension of this movement. When you've got big strong muscles it's crazy how they will mitigate the pain in that joint. It's also crazy that most of the guys I know with amazing VMO development can do these without pain.
There's probably some relationship here with the fact that they didn't spend decades wearing knee wraps, and actually allowed the VMO to fully develop by using a full range of motion in their quad-dominant movements. Crazy talk, I know.
One complaint about the sissy squat is that it's unloading the posterior chain completely and shifts the loading (bodyweight) entirely to the quads. And this is bad how? Yeah, it's called a quad-dominant movement for a reason. Give 'em a shot.