I have had some positive experiences with peer review and some downright annoying ones. I wrote a paper of the relationship between Metaphysics and Quantum Mechanics which went through a number of iterations before acceptance. Initially, the rejections contained constructive criticism that made the work better. But then I got a rejection where the reviewer just didn't like the cut of my jib. About the only objection this person had was to an a footnote I had about Bohmian mechanics and the implications of some experimental tests. I figured that, if that was the best they could do, then the paper was ready to be published. I chose the next journal carefully and it was published.

I am now in a strange situation trying to get a paper published on a type of cancer treatment modality. I am coming from the perspective of a computer programmer, so my proposal is just too different from what the typical oncologist is used to. So they are leery of accepting it. Consequently, one editor told me that they had submitted the paper to 40 reviewers, all of whom refused to review it. They didn't reject it - they just would not touch it. Finally, a reviewer wrote a negative review that had only a couple of nit-picking objections, so the editor felt obligated to reject it. I changed a couple of paragraphs and I'm in the process of submitting to another journal, but facing the same problem.

Sometimes peer review has problems distinguishing between bad science and good science whose novelty is of a degree that it is hard to compare to the rest of the field.