How do I plan for my PhD now that I have graduated with a Masters degree without thesis? A bit of background: I am an Indian citizen with an undergraduate degree in Electronics from India and a Masters degree in Electrical Engineering with a minor in Computer Science (Funny, it is called a minor, given that 60% of my credits are from Computer Science Dept.).

I am currently working as a software developer with a company in Boston, MA. I was involved in some research work during my grad school, but however, nothing materialized and I decided to graduate with a coursework only option (with many projects as a part of coursework). Needless to say, I burnt a lot of bridges along the way which eliminated even the minutest chance for a strong letter of recommendation. 

I wish to, however, apply for a PhD in Machine Learning and/or Algorithms, at least 2 to 3 years from now. The job I am at currently is not a research oriented job. I am doing a bit of research by myself with the data sets available online. 

Given that all of the PhD applications in the US, most in Europe need strong letters of recommendations, if not publications, how can I now set things straight in the coming years. What should be an ideal line of action and is a PhD with a good adviser, possible, at all? 

Note: I am currently working on some Machine Learning related open problems on large data sets, but I am not sure how much can I get done, while working full time in a non academic environment.  Also, I do not have any reputable papers as yet.
Probably the most important thing what you can do to make some doors open is to write a peer-reviewed research paper. 

If you have any chances, find someone in academia, try to structure your interest and do some bit of research which you can publish under the academic. 

Form another point, I know there are some Universities, which value "business" contacts and experience. Don't give up and apply, apply, apply...