When submitting to a directory, the major hindrance as well as the major benefit lies in the human editor. Your submission will be viewed by an actual person who determines how relevant and unique your website is. After passing his scrutiny and editing, your website will be accepted in the directory. This automatically establishes the credibility of your website; hence search engines will consider links submitted to directories.
I don’t think you need to submit to thousands of directories. Search engines no more suggest directory submission for link building. It will be better to choose some quality directories and try to get some quality one way links from other sources.
