Eddie, besides the brace that WantingMuscle mentioned you can also applie ice to the painful joints which should help a lot.

Are you letting your wrists bend too much during arm exercise. Either because they are two weak or because you're just not aware of it? And did you mean just one wrist?

You could have a sprain (strained or pulled ligament) in which case you do need to take it easy, use the brace and ice and let it heal. Don't try to work thru an injury like that. Even when it seems to get better it can come back to haunt you in a big way.

Otherwise, maybe some forearm strengthening and stretching is in order.

As for the knee pain, when it comes to squat it's usually either a form issue or a flexibility issue.

You need to be squating all the way down. No parallels or just past parallel. This puts tremendous pressure on the knees and can actually lead to injury - the opposite of what a lot of people out there think. Make sure your toes are not turning inward - either keep them pointing straight ahead or slightly out. There's probalbly other pointers others here can help you with.

Stretching, like Chinpiece and Wanting said, is very important. I wouldn't really advise stretching before you squat, though, just a good warmup. Stretch after, when your muscles are still warm. This is when it provides the most benefit.

As for as flexibility, what I'm thinking of here is hip flexibility and ililiotibial band flexibility (ITB runs along outside of the thight). Not knee flexibility. DO NOT do things like hurtler's stretch.

Here are some articles:

http://www.pponline.co.uk/encyc/0814.htm
http://www.nismat.org/ptcor/itb_stretching/
http://www.rice.edu/~jenky/sports/itband.html

Yoga is great, too.

Other things to consider are hydration and whether you are doing high impact cardio.