I'd love to be corrected here as it's not something I've ever researched but rather have accepted it is the way it is.
However, as a common sense guess I'm guessing it has to do with the following;
www.example.com/index.html can be a document about dogs and referred to from external resources.
www.example.com/home.asp could be about cats and also referred to from external resources.
On the other hand, via redirection at the web hosting level;
example.com could be pointed to one set of documents (a website)
www.example.com could be pointed at a separate set of documents (another website)
Most paid analytics platforms are pretty expensive to my knowledge. One free tool that will show you live data is Woopra. Having said that you get what you pay for and the data available is nowhere near as comprehensive as Google Analytics.
It's a new algorithm Google rolled out on April 24th this year that targets sites with links from questionable web sites. An example would be a website that has a lot of their links coming from the footer links of other sites, or a link on every page of another site, it looks suspect as far as Google are concerned.