I have been considering taking drastic steps that in theroy would take all links to my domain away in one step.
Modify the DNS CNAME, removing the www to @. This will mean everyone including Google will get a 404 for the site url with www, (which most of my links point to) but sitename . com without www. will display and be available
Has anyone ever done this? I do not want to start a new site as the domain I have is my company name.
[edited by: tedster at 4:01 am (utc) on Feb 22, 2013] [edit reason] moved from another location [/edit]
Essentially, as confirmed by Google's John Mueller, Google still treats the website as a whole algorithmically. Obviously the links pointing to one version or the other (and setting preferred version in WMT) helps a bit but there are still overriding associations which you can't shed.
What happened to me is that I was caught up in this associative part of the algorithm. Some time afterwards I was given a manual penalty for exactly the same reason despite me having no unnatural links pointing to the non-www version of the site. I ended up getting a new domain in the end (different TLD) and haven't looked back.