Can research papers be mentioned as projects in a cv? While working as a research associate at an institute, I contributed to a research project through it's development and experimentation phases. From my contributions on this project I was listed as a second author on some research papers. 

How should I list these papers on my CV, independently or in relation to this research project?
It cannot be a research paper without a project. Research papers are for describing the results of the projects. Even review articles represent projects to collect the information about the current status in the particular branch of the science.

Once you are a co-author, you have been involved into that project. Co-authorship always assumes significant enough involvement. Hope this answers your question.