My friend Chris emailed me this: "... I've often wondered about the logic behind a Zen prayer. Zen and other branches of Buddhism are atheistic. Buddhism is an atheistic philosophy. Why do Zennists pray? Who do they pray to? That doesn't make sense..."
I agree, in a way. It doesn't make sense if we consider 'prayer' to be 'to' another being, ie. a Deity. Zen is basically Atheistic (nothing in Eastern religion is perfectly clear-cut). They certainly don't believe in a 'creator' God like that of Western monotheism. But they're probably going to believe in a 'Pure Land' resided over by a 'radiant, pure, enlightened being' like Amitabha/Amida, the future Buddha of the West. And they'll certainly believe in 'Buddha-Nature', the idea that our true nature is innately pure and radiant, and that it is our mistaken understanding of things that obscures this true, luminous, already enlightened nature.
So, back to prayer. The 'prayer' that a Zen practitioner does is perhaps an attempt to come closer to realizing his/her own already-enlightened nature. A prayer will generally be used to offset some imbalance the practitioner sees in his/her own life, such as a strong, unhealthy attraction to something (thus praying for contentment and to see the impermanence in all things) or an aversion (thus praying for good toward or appreciation of that which he/she is adverse to).
So, perhaps in Zen style, we can say a prayer of good-will to GW Bush, Osama Bin Laden, or whoever else out there we feel excessively repulsed by. And we can say a Zen prayer for equanimity in the face of alcoholic, gluttonous, or improper sexual opportunities.
For me... well, may I be earnest in my studies these next few weeks and hopeful for the health and good fortune of the new Pope, Benedict XVI.