I know that the different color pins have different effects on the brakes and that some of you mix them to fine tune performance.  Can someone explain how they work compared to each other?

Why are there more than one color of break weights for my Baitcasting VBS system?

Shimano makes two different break weights; Heavy (Black, Grey, or Green in color) and Light (Red, Blue, and Clear in color). Most of the new reels are shipped with the light break weights on the reel, and the heavy break weights in packaging in the box. If the light break weights don't provide adequate spool stopping power, change them simply by pulling them off of the spool and replace them with the heavier weights.

http://fish.shimano.com/publish/content/global_fish/en/us/index/customer_service0/FAQ.html

I thought there was a difference between the red and clear.  According to that they are the same.

Can they be mixed, or does the reel need all of the same weight for balalnce?

I thought there was a difference between the red and clear. According to that they are the same.

Can they be mixed, or does the reel need all of the same weight for balalnce?

Yes, they certainly can to help you achieve your desired braking pattern.  My experience is that the default brakes that came stock has covered every situation I face. I've been too lazy to see if adding a few heavier ones could help in throwing 1/8 oz lures better. Curados seem to handle them alright with the defaults.