Including a site to a Web Directory
Web Directory as the word implies is a directory that specialises in linking to other web sites and having those links in categories. Not to be mistaken a web directory, is not a search engine. In a web directory you can do a manual entry and not expect it to find your site on its own. It is one of the starting steps in increasing your links, without having to do a link exchange.

Difference between web directories and link pools
A link pool is similar to a web directory, with the difference that the links are not categorised. Including your site in a link pool can only harm it. For example a Link pool would be a list of links in a hosting or design site. If the other links are not similar to the content of your site, this could possibly harm your ranking. Including your site in a directory is always usefull, but be carefull to submit your site in proper web directories and not link pools. To be understood better a web directory can be taken as the yellow pages for internet.

Web Directories listing categories
There are different ways web directories lists sites. These can be the following:
  Free submission - Lists a website for free
  Paid Submission - Similar to pay per click advertisment
  Featured listing - Getting a paid premium position on a top page (as index page)
  Affiliate links - The directory earns commision for reffered customers
  Reciprocal link - A link back to the directory is demanded, in orger to get listed
  No follow - Adding a nofollow attribute so search engines do not follow the link

From the top list, only two of them can affect you negatively or not affect you at all. Reciprocal links can damage your ranking and a No follow attribute would be as not having the listing at all (concerning the search engines ranking).

Today submitting a web site to a web directory is considered a common SEO (search engine optimisation) technique to get back-links for the submitted web site.