Leg day induces tremendous pressure on your knees.
The most common knee pain experienced by an athlete and or weight lifter is called patellar pain syndrome. It results from wear and tear, which softens the cartilage ("Patellofemoral Pain Syndrome." WebMD. 28 May 2005. Healthwise, Inc. 30 Nov. 2005 <http://www.webmd.com/hw/joint_problems/tp22236.asp>.).
A popping sound occurring in your knees is a warning sound. Keep an eye out for pain, swelling, and locking of the knee joint. These are signs of a cartilage tear (Dinibule, Md, N. (2006, April). Injury Rx: Ask the Doc. Muscle and Fitness, 56.).
Here is how you can ensure long-term healthy joints and reduce knee your agonizing knee pain from previous injuries.
Instead of beginning with the squat...
Start off with a warm up on the bike for 5 minutes
Performing two light sets of 15 reps on the knee extension machine
Perform 3 to 4 sets on the leg press
Perform your regular squat routine followed by your other favorite leg exercises
Stretch your leg muscles for 10 minutes
End with a 5-10 minute bike ride
Tips during the lifts
Never allow your knees to pass your toes
Point your feet outward slightly during the squat, leg press, front squat, ect.
Focus on form rather than the weight
Relationship between the Hamstrings and the Quadriceps
It is generally accepted that the strength between the quadriceps and hamstrings should be equally just like the fact that your lower back muscles should be as developed as your abdominals.
However, because the quadriceps have larger muscle bellies than the hamstrings the quadriceps should be slightly stronger. I would not worry about this too much though since the quadriceps are already naturally stronger (Hatfield, PhD, Frederick C. Fitness: The Complete Guide. 8.1.5th ed. Santa Barbara: International Sports and Sciences, 2004. 169-170.).
Your biggest concern should be developing the both sides of your quadriceps muscles in order to stabilize the knee more. Make sure that the vastus lateralis and the vastus medialis both get a sufficient amount of work.
Organizing your leg routine
Lifting legs once a week seems to make sense in a bodybuilder’s routine, however it is not great for your knees.
Either perform quad and hamstring exercises on different days or if this is not possible then perform the squat or the leg press exercise at the end of your chest and or shoulder workout. This keeps your knees fresh throughout the week preparing them for their next workout (Stiefel, Steve. "Sore Loser." Muscle and Fitness Dec. 2005: 70.)