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.
The leading search engines, such as Google, Bing and Yahoo!, use crawlers to find pages for their algorithmic search results. Pages that are linked from other search engine indexed pages do not need to be submitted because they are found automatically. The Yahoo! Directory and DMOZ, two major directories which closed in 2014 and 2017 respectively, both required manual submission and human editorial review. Google offers Google Search Console, for which an XML Sitemap feed can be created and submitted for free to ensure that all pages are found, especially pages that are not discoverable by automatically following links in addition to their URL submission console. Yahoo! formerly operated a paid submission service that guaranteed crawling for a cost per click; however, this practice was discontinued in 2009.