I sent out probably 8 letters to judges and got 3 interviews. I don't know if my cover letter had any impact, positive or negative, but the format was basically:
Please consider my application for a clerkship in your chambers, beginning in 2008.
Short paragraph (3 sentences) on why I want the clerkship, including interests specific to the court if possible.
Short paragraph on why I'm competitive - one sentence citing some stuff in list form from my resume which I think is applicable to being a good clerk (i.e. I interned with a judge before, etc) and another sentence again with a list of academic highlights (I'm in the top X%, on Blah Blah Review).
Short logistical paragraph -- inlcuded with this letter you should find X; our career services should send you Y.
Final Thanks and request for interview.