I run a free classifieds website http://www.Jihoy.com, and it seems to me that ads aren't very good at attracting links. So I have decided to create more contents by building an article directory into my site. And began bookmarking 1 or 2 articles a day to social bookmarking sites. It seems to me, while those articles are on inner pages of my site, my main page's SERP on its keywords are being affected. I am not sure what is going on. If bookmarking articles in inner pages that aren't directly related to my niche keywords "free classifieds", my main page's SERP falls 3 to 5 positions or more? Am I being paranoid? Is google confusing those articles and reshuffing my SERP because of their contents? As with article directories, I have tons of different categories, maybe Googlebot got confused?
Personally I don't think adding an article directory to a website would help rankings much. If those were all unique articles, then it would help but most article directories are full of duplicate content. All of those extra external links may be harmful to your rankings too. With seo you can't always assume that result x is caused by action y. There are many different factors for determining rankings. It just sounds like your link profile is not strong enough to get stable rankings. This is very common when a website does not have good enough links. Websites can do quite well while targeting many different topics. So I don't think some unrelated links would harm your rankings much. If they did harm your rankings, sites like wikipedia would be sol. Sites that stick to just one niche can likely get rankings easier though.