It has cleared that Google now treats www.yourdomain.com, yourdomain.com, and yourdomain.com/index.html as different websites, the effect of which is that these pages are treated with goggle as different web pages with same content and these pages are penalized for this fact. This is a basic indexing issue and its problem with goggles indexing capability that it was unable to resolve this issue. (all the above is purely my speculations and observations - you are perfectly welcome to think its a load of crap).
Also if you use Google Webmaster Tools you can tell Google which version you would prefer indexing, with or without the www.
For www.yourdomain.com and yourdomain.com, you can indicate your preference in Google Webmaster Tools. For yourdomain.com/index.html, donot have this as your link to homepage. Instead use either www.yourdomain.com or yourdomain.com as per your preference.
This is the way to fix it so that none of the search engines will have this problem with your site. As opposed to using Google webmaster tools which does not fix the issue for Yahoo or MSN. Peace!
Never use Google Webmaster Tools to do this, always use a server side 301 redirect to correct the canonicalization.
One point that has gotten lost in the discussion of canonicalization issues is that Google does eventually resolve them on its own. The problem is that 'eventually' can take several months, which can feel like an eternity if its your site that's having the problem. I would be much more concerned over the www. subdomain issue than anything to do with index.html|index.htm|index.shtml|index.php versus the root URL issue since the latter is resolved much faster and has far less consequences to your rankings in the meantime. You should certainly use a 301 redirect to make sure the domain name is canonicalized in the format you prefer on all search engines, of course.
Actually I see sites constantly that have been online a very long time over a year or two in some cases, and Google stills sees the site as several different websites. Sorry but Google does not fix the issue on its own. If Google did resolve the issue itself there would not be a need to offer webmasters the ability to choose the preferred URL option in Webmaster Central Canonical URL issue has nothing to do with page naming. Feel free to read & learn more here http://httpd.apache.org/docs/2.2/rewrite/rewrite_guide.html Peace!
Correct, Google will choose which version they "think" is correct to display in the SERP's and this is generally determined by the authority of each URL version. Also Google will still assign different Pagerank values to each URL no matter how long you wait, meaning your incoming links are canonized and you have duplicate page URL's. The best fix is a simple 301 with .htaccess