There definitely is a stigma attached to the use of "nofollow" links. Search engines may publically be seen to deny this stigma; they may even refuse to acknowledge it altogether (for some time); but the fact remains that the use of "nofollow" links does indicate the presence of linking to resources which have not been manually approved as linkworthy.
Webmasters may think they're being clever by telling search engines that they don't endorse the sites which they link to, but in actual fact they're also doing themselves a contrary disservice by telling search engines that they're pointing human users to unwelcoming or irrelevant or otherwise untrusted resources.
I'm not saying don't use nofollow on untrusted links. I'm saying don't use untrusted links. But if you do make the mistake of linking to untrusted resources, don't just use nofollow in the markup; try to use CSS which tells human users the same info as you're giving to search engines. For example, for all within div#style1, to make standard links blue, unendorsed links orange, and especially endorsed links green:
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml"
lang="en-GB" xml:lang="en-GB">
<head>
<title>Example></title>
<style type="text/css">
div#style1 a{color:#0000FF;background-color:#FFFFFF;font-weight:bold}
div#style1 a[rel="nofollow"]{color:#FF9900;background-color:#FFFFFF}
div#style1 a[rel="endorsed"]{color:#00FF00;background-color:#FFFFFF}
</style>
</head>
<body>
<div id="style1">
<a href="#">Standard Link</a> |
<a href="#" rel="nofollow">Unendorsed Link</a> |
<a href="#" rel="endorsed">Endorsed Link</a>
</div>
</body>
</html>
Accessibility note
If you use no method but colours, to convey particular information, you won't pass W3C WAI WCAG AAA. Consider also playing with font faces, text decoration and other styles to distinguish between standard links and "nofollow" links.
