QUOTE: “Keyword Stuffed” Main Content Pages may be created to lure search engines and users by repeating keywords over and over again, sometimes in unnatural and unhelpful ways. Such pages are created using words likely to be contained in queries issued by users. Keyword stuffing can range from mildly annoying to users, to complete gibberish. Pages created with the intent of luring search engines and users, rather than providing meaningful MC to help users, should be rated Lowest.” Google Search Quality Evaluator Guidelines 2017
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.
It’s important to note that entire websites don’t rank for keywords — pages do. With big brands, we often see the homepage ranking for many keywords, but for most websites this isn’t usually the case. Many websites receive more organic traffic to pages other than the homepage, which is why it’s so important to diversify your website’s pages by optimizing each for uniquely valuable keywords.

Submit website to directories (limited use). Professional search marketers don’t sub­mit the URL to the major search engines, but it’s possible to do so. A better and faster way is to get links back to your site naturally. Links get your site indexed by the search engines. However, you should submit your URL to directories such as Yahoo! (paid), Business.com (paid) and DMOZ (free). Some may choose to include AdSense (google.com/adsense) scripts on a new site to get their Google Media bot to visit. It will likely get your pages indexed quickly.