ahyes,
The common view of nutrition often revolves around the prevention of deficiency states. You know the drill: vitamin C/scurvy, B1/BeriBeri, vitamin D/rickets, etc. My view, and that of many others, is that nutrition plays a much larger and broader role. This article from 2003 will be of interest to you as someone who has studied some nutrition:
http://www.ajcn.org/content/78/5/912.long
The author, a well-respected nutritional scientist, discusses the concept of "long latency deficiency diseases", which differ from the above-noted "index diseases" associated with nutrient deficiency. As you'll see, he uses calcium and vitamin D as examples, both of which you've already made mention of as worthwhile supplements. However, this paper may at least get you thinking in a different fashion about the role of nutrition in health and disease.