Search engine spiders may have problem reaching deeper pages in a website. So try keeping the most important pages of your website no more than one or two "clicks" away from your index/home page. Goal should be to keep your pages closer to the root instead of deeply-nested subdirectories. By implementing this you will be assured of optimum indexing of your web pages. Just as your website users may become lost and disappoint in too many clicks away from your homepage, the robots may also give up after several clicks away from the root of your site. That is why a deeper pages get fewer link popularity.

Take for granted that most links to a site come in to the default home page, the linking hierarchy is arrange in a pyramid like structure around clicks away from that page. It generally complement how the directories are organized.