I have given up using the squating cage at the JCC on Sunday mornings until I have my MRI and find out exactly what's causing my leg pain. I figure it's best to avoid squating and lunging with 140 lbs of weight on my shoulders for the time being.
But it is still important for me to strengthen my legs, and is actually part of my rehab prescribed by my physiotherapist. So I've tinkered with my workout to come up with challenging exercises I can do that won't irritate my hamstring/glutes.
This is an amazing exercise that I love (because it is effective) and hate (because it's tough). You don't need a weight bench, a chair (not on wheels please!), aerobic step or even a firm bed can work instead. I also like this because it forces you to squat with your knees behind your toes, which is important to protect your knees. I guarantee you will really feel these in your quads and glutes.
Use as much weight as you can. You can start with no weight at all and work your way up. I'm currently using 25 lb dumbells and I try to do 3-6 sets of 15 repetitions. The lower the surface you are squating to, the harder it will be.