The resident bad knee expert ... sad but true.
Mami, I'm not sure what the issues are with your knees, but I can tell you how I've adapted my workouts to deal with my dysfunctional knees and maybe you can get some ideas that work for you. I've had several talks with my doctor about how to adapt exercising because he understands that being fit and active are extremely important to me. The good news is that I'm still doing legs twice a week.
My problem is osteoarthritis - I don't have any cartilage left so am 'bone on bone' (yeah, you can hear the bone on bone

). I also have a ton of bone spurs that limit my range of motion. It feels like I have sheets of metal tightly wrapped around both knees.
In practical terms, it means I can't do impact activities and anything that requires bending the knee to 90 degrees. Plyometrics are out, as are step ups and lunges (I just can't get to that perfect 90 degree angle with the front and back leg any more). I'm still doing half-baked squats but not down to 90 degrees.
So I do a lot of leg press, sometimes one-legged (one knee is worse than the other and I worry about that leg getting weaker). Our gym has sitting, lying, and 45 degree leg press and I use them all. When you change your foot position, like Mel suggested, it will target different muscles. Try feet together, shoulder width apart, and in a plie position.
I use the hack squat machine, stopping just short of 90 degrees. There's debate about the merits of the leg extension machine, but my doctor suggested it so I use it one leg at a time (it's fun to do five sets in a row, just switching back and forth from one leg to the other). I also use the seated leg curl machine (I don't have enough range of motion for the lying one).
Have you tried ball squats, using an exercise ball behind your back against a wall? Those work for me so long as I stop short of 90 degrees (remember to have your feet out far enough so you keep your knees behind your toes). You can do high rep sets - like 50+ - and/or add weight by holding DBs.
Other fun exercises using the ball ... lie on your stomach on a ball and do leg lifts up in the air or scissor your legs back and forth (squeeze your butt on both).
Your gym probably has other odds and ends of leg machines ... check 'em out and see which are comfortable for you.
Stiff legged dead lifts (like you described) are a staple for me. If you want to take your lower back out of the picture and make it more of a hamstring exercise, stop as soon as you feel the stretch in your hamstrings. When you go too low it becomes more of a lower back exercise. Squeeze your butt and focus on pulling yourself up with your legs and butt, not back. This exercise needs to be done s-l-o-w-l-y and with a lot of focus. Have you ever tried it with a BB instead of a DB? Much easier, IMO.
BTW, the Smith machine is notoriously hard on knees. I don't understand the physics, but it has to do with shearing force. Most people with knee problems avoid it like the plague (as do many people without knee problems

).
Geez, I rambled and wrote a book.

Let me go away and see if anything else comes to mind ...