At one point in the film, Jen must discern the real crystal from three identical looking shards. He succeeds in doing this by playing a note on his flute, which causes the middle crystal to glow with light. This is indicative of the importance of the Middle Way, in Eastern Buddhism.
The characteristic differences between the Skeksis and Mystics could be interpreted as an allusion to the different philosophies described by Eastern and Western thought. The selfish and materialist Skeksis could be taken to represent Western Capitalist modalities, while the natural, peace-loving Mystics to represent the Eastern Religious Philosophies. The film, therefore, tries to show that only a union between these two polar opposites will bring an end to suffering, as neither philosophy is fully complete without knowledge of the other.
The union between the Skeksis and the Mystics must take place before the Great Conjunction when the triple Sun shines One. I believe that the course of events on Earth has been gearing us up towards the alchemical union of these two systems, and that it will begin in 2012, bringing about a Golden Age of Enlightenment.
A sequel to the Dark Crystal, called The Power of the Dark Crystal is set to come out sometime this year.