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Google, Bing, Yahoo, Ask, Alexa, etc. will always show links coming through even if they're nofollow. The difference is that the link which is nofollowed will not pass any "link juice" to the site you're linking to. If you're using nofollow correctly, this shouldn't matter.
E.G. Google's Knol is nofollow (unless you have some stranga algorithmic permisssion no-one seems to be able to nail down) bu they'll always show up as links in your webmaster tools.
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