So we have been ranking #1 on Google for a page (say /page1.html ). Since this page is linked more than once on the Homepage and other high traffic pages, we found it logical to add a reference parameter at the end of the URL.
So, the anchor link to the page from the sidebar became /page1.html?ref=sidebar, the one on the navigation became /page1.html?ref=nav,etc. Now during the same period, the average ranking of the page on Google has dropped from around 1.1 on the Webmastertools to around 2.5.
I'm not sure if this could be one of the reasons. The drop in the SERPs has not been drastic, so I am not able to absolutely confirm the specific change that has caused the drop, but I would be interested to learn if this reference tagging could have an effect on the ranking.