As quoted by Aaron " The key to ranking well in search engines is getting natural citations" . Search Engines like websites who have natural link profile. One pecularity of natural links is that they are spread to different pages on your website. When a website has all the backlinks pointed to its homepage, it is easy for the search engine to make out that the links are artificial. This is what is called the "Deep Link Ratio". Basically it is the ratio of the number of "deep links" a website has to the number of backlinks to the home page of the website.

The lower the ratio the better. You can use this free link harvestor tool to find your Deep Link Ratio and compare it with the one of your competitors. This version is for a trial. If you are a heavy user please download the source code here and you can put it on your own server.