I recently discovered this method of clearing crystals
http://www.youtube.com/watch?v=M5b9uD7JFhE&feature=related and find it quick and effective. Have also been experimenting with placing them in my Tibetan singing bowls and using the bowls' vibrations to clear them. Again, this seems to be very effective. Enjoyable, too!
hrm...I think I prefer the water method,I like the idea of using each of the elements in it's own way to purify and decontaminate the stones. also,not all of them are crystals. I don't know if that makes a matter to the sound method working or not.
also to the person who posted about the colours fading,my stones never see the light of day,I only ever charge them with moon light or dark of moon energy.