I always thought following links are same -
http://ganeshhs.com/search-engine-optimization-seo/noindex-nofollow
http://www.ganeshhs.com/search-engine-optimization-seo/noindex-nofollow

Above links leads to the same page, but it differs with www.
But search engine treats both links are different, i have seen in few cases where we link many a times we ignore www. and in some cases we do include www. in the links.

So what are the impacts?

1. Search engines keep both the versions of the URLs, when people click on search engine results links which leads to our site with different versions of these URLs, it will drastically affect the page rank and traffic.
2. These URLs look like different documents to crawlers and create excessive crawling on our website.

How do we instruct search engine to treat both the URL’s as same, Google webmasters tool has a option to set the preferred domain

So whats the advantage of set preferred domain ? If i set my preferred domain as ganeshhs.com and next time if Google comes and crawls my website, and if it finds any link starting with www.ganeshhs.com it will follow it as ganeshhs.com and when Google displays my website links in search results it will show the links as ganeshhs.com

It also helps us to fix the external site referrals,  few guys started provide links to my website, if suppose their referral link is http://www.ganeshhs.com/category/search-engine-optimization-seo where as my actual article URL was http://ganeshhs.com/category/search-engine-optimization-seo and when google crawls our website through that referral link it will keep the right version of domain what we preferred.