I was honest (and I felt I knew my son pretty well). I was certain that his weaknesses would also be mentioned in teacher reports, etc.
I think I mentioned disorganization and lack of the ability to set priorities and time management -- but I also stated that he was very interested in improving these areas and one of the reasons he wanted to attend boarding school was the required study hall periods (which he also mentioned in his essay). In his essay, he said it was hard to be motivated to study when none of the kids he hung out with did any studying. I also said that this weakness was one of the reasons our family felt BS was the best placement -- even without any studying or time management, he could still get great grades (including A's from papers written in the 15 minutes before class started over lunch).
I think I also said that I was concerned about his writing skills -- and that his current school had the kids write one paper a semester.
So -- for my kid, it was academics. He really didn't have any weaknesses in other areas, but that might not be true for other kids.
I think the key is to be honest, yet explain the reasons behind the weakness and why BS is the answer to overcoming it.
Of course, if your kid has some serious character flaws (likes to torture small animals, shoplifts regularly, beats up his mother), you might have more trouble (read that last sentence with a sarcastic tone).