For those of you wondering how this affects the other search engines that support the Sitemap Protocol, rest assured that we're talking to them about how to make cross-submissions work seamlessly across all of them. Until then, this specific solution will work only for users of Google Webmaster Tools.
Selecting pages to appear as sitelinks is a completely automated process. Our algorithms parse the structure and content of websites and identify pages that provide fast navigation and relevant information for the user's query. Since our algorithms consider several factors to generate sitelinks, not all websites have them.
Now, Webmaster Tools lets you view potential sitelinks for your site and block the ones you don't want to appear in Google search results. Because sitelinks are extremely useful in helping users navigate your site, we don't typically recommend blocking them. However, occasionally you might want to exclude a page from your sitelinks, for example: a page that has become outdated or unavailable, or a page that contains information you don't want emphasized to users. Once you block a page, it won't appear as a sitelink for 90 days unless you choose to unblock it sooner. It may take a week or so to remove a page from your sitelinks, but we are working on making this process faster.
To view and manage your sitelinks, go to the Webmaster Tools Dashboard and click the site you want. In the left menu click Links, then click Sitelinks. Thanks for your feedback and stay tuned for more updates!
Update: the user-interface for this feature has changed. For more information, please see the Sitelinks Help Center article.
