If you are looking exactly reason though which search engine takes decision for any link then I want to say you clearly that,No one can be actually certain of what accurately it takes to search out on top of the search engine results. There are a huge number of factors concerned. On the other hand, it has been well-known for a fact that all search engines gives value the importance of links.
This is referenced from Google’s Guidelines for Webmasters:
When your site is ready completely: Have other related sites link to yours.
This is referenced from Yahoo’s guidelines
Keep up a correspondence with webmasters and other content providers and build wealthy linkages between connected pages.
Since it is obvious that links are essential, the question is ‘do directory links count up as well?’ Well, this is to quote another pointer from Google’s Guidelines for Webmasters and you have to choose Seo-friendly directory for sure about doubt related to your question:
Suggest (submit) your site to related directories such as the Open Directory assignment and Yahoo!, as well as to other industry-specific expert sites.
You have to make sure in some area to influence your search engine ranking, if you know a bit about search engine tips then you will know sure that Guidelines of Google tell that you must submit your site to appropriate directories. What makes a directory related to your site? Well, there are a number of common directories out there that include sites from all categories. So would these directories be counted as relevant directories? Well, they would to a certain extent, if there was an available category related in some way to your subject of site. Placing your link in a applicable category in a general web directory will help search engines categorize the main subject of your site and the link would count, to a positive level, in influencing your search engine rankings.
The fundamental principle is that while submitting your site to seo-friendly web directories will not damage your site in any method, the directory links will on the different help put up your site’s link reputation which can only be more supportive (helpful) than destructive(harmful) in your search engine ranking efforts.
Given the fact that good number universal web directories are free to submit to and there being quite a small number of seo manual directory submission services similar to ours that will help save you the time in submitting your site, there is not any real reason for you not to have your site submitted.