You can confer some of your site's reputation to another site when your site links to it. Sometimes users can take advantage of this by adding links to their own site in your comment sections or message boards. Or sometimes you might mention a site in a negative way and don't want to confer any of your reputation upon it. For example, imagine that you're writing a blog post on the topic of comment spamming and you want to call out a site that recently comment spammed your blog. You want to warn others of the site, so you include the link to it in your content; however, you certainly don't want to give the site some of your reputation from your link. This would be a good time to use nofollow.