At the Huffingon Post, BJC General Counsel K. Hollyn Hollman offers the best critique I've read yet of the National Day of Prayer. Here's a snippet, but go read the whole thing.
There is no problem when Americans — including public officials — gather to pray. In fact, for people of faith, every day should be a day of prayer. Questions properly arise, however, when the government, by an official act of Congress, urges citizens to engage in a religious exercise. As citizens, Americans share a long history and proud tradition of religious liberty. As individuals with diverse beliefs, however, Americans do not share a common religion or participate in the same religious practices. A day of prayer might be appropriately encouraged by our country's various religious leaders — but it should not be called for by civil magistrates, Congress, or even the president.