To quote series creator Vince Gilligan:
We had this instinct that it would be helpful to have something distinctive about Walt’s product. And we figured it should be nice and clear and not cloudy that a proper product would be.
We thought yellow would be a terrible choice because it would remind people of urine, and we figured green would be an odd color and we thought blue was a good choice because it feels clean.
We called up (science consultant) Dr. Donna with our fingers crossed, asked her if she thought it was possible for this product to come out as blue. She looked into it and said not really, and in fact, if you add a color, chemically speaking it would mean the product is probably less pure and been adulterated. And that worried me when I heard that.
But she said, you know at the end of the day this is a fictional story and I’ll help you get the chemistry as right as I can. Sometimes technical advisors will be very rigid and say it will never work that way, never in a million years, but she was very good that way.