TyMax - 8:41 pm on Mar 30, 2011 (gmt 0) [edited by: tedster at 10:31 pm (utc) on Mar 30, 2011]
I have had this problem with htm pages as well and I believe it is someone trying to sabotage my ranking by producing duplicate content to some of my better indexed pages.
I found this out when a page was no longer being indexed by Google and found the duplicate page which I think has at least one canonical link to it from another website not mine. The person is putting this onto the end of the url.
The 404 will not filter out the ?ref=*****.Com and Google still picks it up. I set up Parameters in Google Webmaster tools to disregard the ?ref=*****.Com but it still seems to pick it up. Google now picks up the main page as the primary and seems for now to disregard ?ref=*****.Com
You might want to try the Parameters in Google to filter out the string. You might want to read this page which explains the problem.
I did not want to go through all the 301 redirects. Try putting ?ref=*****.Com in Google and see how many pages still come up. Put it on one of your .htm and .php pages and see what I mean. Seems it maybe a new tool others are using to try and sabotage other website page ranking.
[edit reason] hide the domain name [/edit]
[edited by: tedster at 10:31 pm (utc) on Mar 30, 2011]