First: Equality California's got a nice form letter to send to the President here.
Second: use http://www.whitehouse.gov/contact/ to send a message to the President. Here's what I sent; you can totally riff off of this:
Dear Mr. President,
I was dismayed when I found out that the Department of Justice had filed a motion to dismiss Smelt and Hammer’s suit contesting the constitutionality of the Defense of Marriage Act. During your campaign, you pledged to work to overturn this Act. However, this dismay is overshadowed by the shocking and appalling content of the motion.
The motion in question compares same-sex marriage to incest and polygamy. It also claims that persons who are deeply in love with a person of their own sex should marry persons they do not love of the opposite sex merely to obtain the benefits of marriage.
Your presidency has been compared to that of John F. Kennedy. Like Kennedy, you have promised much to a historically disadvantaged group of American citizens. However, I hope that unlike Kennedy, you actually manage to effect real change during your administration.
I ask you to instruct the Justice Department to withdraw this insulting motion. Until then, Mr. President, you have lost my support.
Your fellow citizen,