Would rel="canonical" be the best way to avoid duplicate content?

Selected answers from the Dumb SEO Questions Facebook & G+ community.

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  Arseniy Bolotsko: I am working on organizing about 3000 article for a new WP site launch. All article have been sorted and categorized in a very simple/intuitive way. My SEO concerns include duplicate content, category v.s. tags (or using both) and canonical urls. ;
  
  Articles are divided into 3 primary section ;(Magazine, E-publications and Opinion Columns) which is pretty simple to work with. For UX reasons I would also like to display articles from every category under 1 of 8 Market Segment categories i.e. all articles from "Magazine, "E-pub" and "Opinion Column" sections that are about "Green Energy" will display under market segment called "Green Energy" but they will retain original URLs. Lastly, each article will only be associated with one Market Segment.
  
  Based on this scenario, what will be most beneficial from SEO perspective? ;Would rel="canonical" be the best way to avoid duplicate content? Crawl Noidex Market Segment category pages?Are there any other potential pitfalls I should look into?
  
  P.S.
  
  Attached is a very quick diagram I put together to visualize the process ;
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  Jim Munro: I think that might be the best-documented question we have seen here, +Arseniy Bolotsko ;. I hope you get some great responses. :)
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  Arseniy Bolotsko: +Jim Munro ;my good old friend! Having been around much lately so I figured I should contribute.