If you are putting some effort into building up the number of links to your website, you may be interested to learn more about how search engines see links.
Not all links are created equally. In some cases there are technical reasons why search engines may not pick up on a link that you might think they should. Applying the nofollow tag to a link is one reason, but there are others.
This article by Gyutae Park explains how it all works: How To Confidently Build Links that Pass SEO Value.
Note: the article is quite technical in places – but so are search engines.