Yeah my knees can be pretty bad too... With the muscles - no pain, no gain, for sure. But when it comes to joints you have to be really careful. You could be headed for a knee injury, which you DON'T want! It doesn't necessarily mean don't do the exercises, it just means a) make extra-sure that you're using good form (particularly on squats, make sure that your knees are going out in the same direction that your toes are pointing, and b) if it hurts (like injury-type hurt - make sure you can tell the difference between a muscle burn and a joint pain - you probably can but just in case ) stop and rest the area for a few days. Icing it helps. So do lighter strength exercises to work up the muuscles in the quads (thighs) which support the knees.
Also, when I'm squatting heavy I usually wear a knee-brace, just a thickish nylon thing I picked up at the drug store. That seems to help.
Here's a really good page on working with knee pain with lots of tips and such: web page HTH!
Posts
Re: Ouch! Knee Pain from strength exercises
) stop and rest the area for a few days. Icing it helps. So do lighter strength exercises to work up the muuscles in the quads (thighs) which support the knees. 
