Carl Burgchardt in Speech Communications speaks eloquently of his goals as he comments in the margins of students' papers. He attempts, he says, "to emulate a dialogue..., to show an intelligent mind engaged with the text." He tries to frame comments as questions to reinforce that dialogue.
He also notes that based on long experience he has found that he gets the best results with students when he spends his time discussing the assignment and what it calls for. He helps students define the task and strategies for tackling it. And he often provides students with a sample paper and critique to show them how to read his dialogue in the margins and to benefit from seeing what other students have done.
He notes finally that he always asks himself if he's written anything on the paper that he wouldn't want to have the student's mom read. His margin notes are clearer and more helpful when he keeps that rule of thumb in mind.