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.
Fortunately, Google puts more weight on the anchor text of external links anyway. So as long as some of your external links have your target anchors, you’re probably OK with a “Home” button. In fact, I’ve ranked homepages with a “Home” anchor text nav button for some seriously competitive terms. So it’s not a make-or-break ranking signal by any means.
Black hat SEO involves techniques such as paying to post links to a website on link farms, stuffing the metadata with nonrelated keywords, and using text that is invisible to readers to attract search engines. These and many other black hat SEO tactics may boost traffic, but search engines frown on the use of such measures. Search engines may punish sites that employ these methods by reducing their page rank or delisting them from search results.

Lastly, it's important to remember that paralysis by over-thinking is a real issue some struggle with. There's no pill for it (yet). Predicting perfection is a fool's errand. Get as close as you can within a reasonable timeframe, and prepare for future iteration. If you're traveling through your plan and determine a soft spot at any time, simply pivot. It's many hours of upfront work to get your strategy built, but it's not too hard to tweak as you go.