What is a correct way for "marketing" non core PhD achievements on a CV? Reading this question and its answers got me thinking, once non-core PhD skills are learned and perhaps mastered, how can we make these achievements clear on a CV when applying for academic positions?

For example, my PhD majors in atmospheric physics and photobiology, but a significant part of it is in Android programming (the basis of the 3 published papers so far) and a few other skills not directly related to the major disciplines, but important nonetheless.

Related, would having peer reviewed published papers be considered as proficiency in the non core subjects without taking away the focus from the major disciplines?
I see no reason at all to leave any reasonable skill or ability off of your CV. Play a musical instrument? Won some medals in a sporting event? Program an android app? Have a black belt in a martial art? Add a section called "Other skills" or "Personal Information" and briefly list these skills. There are two reasons for this. First, it can help a potential employer think of you as a real person, perhaps someone they would like to know. Second, many skills can take years of dedicated practice to master; if you can master one such skill, then there is a good chance you can master whatever new skills may be required in the new job. 

Here is an example from my life. Many years ago I programmed a video game (one of the old "text adventure" style games. I placed this on my CV, not thinking much about it. It turned out that one of the elder faculty conducting the interview had played that game and remembered it fondly. This alone certainly did not "get me the job," but anything that can smooth the way can be helpful.