Not sure what sites you're referring to, but the word "update" is time-sensitive... IE9 is now current, and IE10 is just around the corner (IE9 is only available in Vista and above, and IE10 in Windows 8).
It's also possible that settings you've changed or limitations that your security software is applying may be blocking functionality for certain sites, causing them to put up that message. Are you willing to share a link here to a site that's
complaining about your needing to update?
You can return Internet Explorer to all default settings via a fairly simple process. Go into Tools - Internet Options - Advanced, and look for the [ Reset... ] button.
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