How to react to flawed preprints? Suppose you were to find what you think are serious flaws in a preprint (arXiv or something similar). What should you do? Now, after the obvious first step of contacting the authors and letting them know, what should you do if you were basically told off ("thanks for your interest" without addressing any of the technical concerns)? 

Were this a regular journal, one might write a letter to the editor, or a comment (one might go this route even without contacting the authors in the first place), but how should you deal with preprints, whose contents is in a way still evolving? Would a "comment" paper uploaded to the preprint server not be considered rather aggressive (I don't remember seeing anyone doing this)? Is there anything one can, or should, do before the (eventual) publication of the paper in some peer-reviewed venue?

Stretching this well into the hypothetical, suppose that one did write a "comment" paper and uploaded it onto the preprint server. Would the authors of the original preprint be ethically obliged to cite this and address the concerns raised therein when submitting to peer-reviewed journals (assuming that they were to submit after being let known of the existence of the comment)?
You have no need to do anything. By contacting the author, you pointed out what you believe to be a flaw. It could be you are incorrect, it could be that they deal with this in a future version, it could be that they simply don't care. To me, this situation is akin to the following xkcd comic:



People perform research, good and bad, every day. Once it's published you can feel free to write an article refuting their conclusions, but until then it's just informal academic discussion, and there's nothing you can really do about someone else being wrong.

Disclaimer: Some disciplines may treat preprints as actual publications, and if so, the preceding does not apply. I do not know of any fields for which this is the case, but then again, there's a lot of things I do not know.