PhD opportunities when lacking publications This question in some sense, complements  this question. Suppose a good student completes his master's degree in a less-than-top-ranked university. He has excellent academic grades both in his bachelor's and master's, but unfortunately has not experienced the best research 'atmosphere' in his post-grad and so does not have any publications thus far in his career.

It is a hugely relevant practical issue: low-ranked universities woo good students by providing them full funding plus scholarships for their master's, so there are many cases where students prefer them to top colleges where funding is not assured. After completion of graduation, these students desire to go for a PhD in top universities. So the question is this: 


How does a bright student with excellent grades but lacking in publications secure an admit in a top school? 


One obvious answer is to formulate an excellent research problem and to convince professors of his research ideas pertaining to the problem. Any other useful suggestions?
You have to make the case that your research potential outweighs your lack of research output.

The only places to make that case are your research statement and your letters.  Both your statement and your letters should make it clear that you are an active researcher, even though you are not yet published.  Your statement should describe the specific research problem(s) that you are pursuing, promising and specific partial results, and a specific and well-informed plan of attack.

Similarly, letters from faculty at your MS department should describe your independence, stubbornness, intellectual maturity, and so on, in specific and credible detail.  When you ask for letters, ask your references specifically if they can write a strong letter about your research potential.  Ideally, your references should admit that their department doesn't provide you with the environment that you need to thrive as a researcher.  And it really hurts to write “[Bravo] can do better than us,” so it better be true.

Admissions committees (at least the ones I've been on) do take applicants' previous institutions into account when judging research records.  We know that  applicants from most 4-year liberal arts colleges don't have as many opportunities for computer science research as applicants from (say) MIT, so our expectations for MIT applicants are higher.  So your lack of publications may not hurt you as much if your MS department is known to have a weak research atmosphere.

However: Do not suggest in your application that your lack of publications is your MS department's fault.  You may believe it's their fault, and you might even be right.  But if you actually write that it's their fault, you'll come across as someone eager to blame others for your weaknesses.  No matter how good you are at research, nobody will admit you if they think you're a jerk.