What University Affiliation should I list on my paper? I wrote a paper with my colleagues at my alma mater, fresh graduated from my undergraduate degree. At that time I had no University Affiliation. Now I'm studying a Masters in ANOTHER university, should I put this new Institution as my Affiliation? or none?
List your new (current) institute as the primary affiliation (i.e. the one that appears under your name on the front page). 
You can optionally add a footnote briefly mentioning the part of the work which was done while you were in your old institute.