If you're going to do that for any browser, phrase it apologetically (sorry that my website sucks on IE6) or encouragingly (upgrade to get better features!), never aggressively ("upgrade from IE because IE sucks!")
And Never, Ever, use an alert message. If you're using an alert message, it's because your website is rubbish. Good websites give feedback inline.
IE6 might be a pile of crud, but your customers probably already know that. Nobody uses it out of choice.
Your website is there to help users. If you're going to punish them for visiting, they won't come back.