Think of it this way, does it look like you put the link there yourself? The site that ranks at the top of Google isn’t the one with the most directory listings. Think about it, who is going to visit a web directory and submit your website because they love it so much? I love visiting nba.com and regularly visit it to look at the latest scores and stats. Am I likely to then visit a directory and add nba.com to its listings? No, of course not! Why would I? Is this something people tend to do?
Then why would Google give your site extra rankings because it has thousands of directory listings (most probably automated!)? Am I saying you will get punished for having hundreds of automated web directory listings? Of course not, and I’m not disregarding the human element of this. Maybe someone might stumble on the directory and click the link to your site. If you are using this method to game the system and outrank your competitors then you might want to rethink your strategy.
The best links are the ones that appear naturally. I’m more likely to see a site I love and then link to it via Twitter, which is why Google is now factoring this into their search algorithm. Social signals are a great way for search engines to see what’s being discussed, why wouldn’t they factor this into their algorithm? If you write an article and it manages to be retweeted 20 times then don’t you think that would mean more than a directory listing? Factor in how many followers these people have that are tweeting about your company and bingo! You now have your head in the game. How are your competitors getting mentioned in tweets? How did they get so many followers? What are you doing to connect with your audience?