I have found that most letters of recommendation are not worth the paper they are printed on because they are almost all uniformly complimentary. They can hurt you in the following ways. If you are applying for GPR and the writer states that they are recommending you for a specialty program (you are applying for both). Another bad sign is if the letter is very short. Finally, anything which is even remotely uncomplementary probably indicates that the person is not good, the writer just doesn't want to come out and say so.
I find the most honest letters come from someone who is a personal friend of mine or who trained with us. These people are not likely to refer someone as good if they are not.