The country has gone through, in effect, three phases. In the first, presidents used a religious-diversity model. From 1937, when the first inaugural prayer was offered, until 1985, the presidents (with one exception in 1981) had clergy of different faiths or denominations up on the podium....
Then in 1989 and 1993 we tried what might be called the "America's pastor" model. One man, the Rev. Billy Graham, offered both the invocation and benediction. He pulled it off by using broadly inclusive language....
Next came the Protestant-only model. In 1997, Mr. Graham was the only pastor at Bill Clinton's second inaugural, but this time he made it a fully Christian prayer, ending it "we pray in the name of the Father, the Son and the Holy Spirit." .... Barack Obama mostly seems focused on ideological rather than denominational diversity.
UPDATE: In Monday's Washington Times, Rev. Franklin Graham (son of Billy Graham) who gave the invocation at George W. Bush's 2001 inauguration adds his thoughts on the issue of inaugural prayer. Graham's 2001 invocation ended with a specifically Christian reference. He urges those on all sides of the issue to "calm down" about it.