For paper based on thesis, should I list my university as affiliation or the name of the company I currently work for? I am currently writing a paper for the thesis work I did last year along with my advisors. (I successfully graduated last year and currently work in a software company.) I am confused regarding what organization I should  mention in the author's section. Should I mention my university name since I completed my thesis work when I was a university student or the name of the company I currently work for?
I will take a somewhat different view from @jakebeal's answer.

The primary question is: when did you work on the paper? Did you do all of the work while you were a thesis student, and then the paper has slowly made its way through the system? Or did you actively work on it as part of your new job? Did you use institutional resources from your new position to do any part of the paper?

If the answer to the latter is no, then you should only list the old institution in the actual affiliations, and then list your new job as a "present address", if you so choose. If you worked on the paper as part of your new job (beyond rote submission and minor edits), then you should list both workplaces as "active" affiliations.