By default, on the store views list (usually for languages), Magento creates links to the different views but it also adds the “from_store” parameter. It seems that SEO guys don’t like this too much.
If you need to remove it, search on your theme templates for the “select_language” string. Usually, this is on the header.phtml, but depending on the theme, it can be placed in other places. So you can look for it using grep:
cd var/app/design/frontend #go to the theme folder grep -r "select_language" ./
You’ll find you phtml with this string. Close to that string you’ll find the function: $_lang->getCurrentUrl(), change it to: $_lang->getCurrentUrl(false).
Note: Indeed, you can look for this function direcly, but try to not modify core files (including core themes).