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It would depend on the purpose of the link directory and if you own the link directory, or if you are a webmaster that wants to post a link on the link directory.
Webmasters seem to prefer link directory websites that do not use "nofollow" attributes on link tags.
Link directories that use directory to use "nofollow" are able gain more of a benefit from the Google PageRank of the websites that are linked within it.
Other factors to consider would include; if directory is part of a website or if the website is a directory.
Webmasters, web developers, internet marketing experts, search engine optimization experts, and online business owners often have different purposes for using a directory.
Some directories are used to promote websites owned by the directory owner.
Some directories are link directory websites are setup to promote websites that are not owned by the directory owner.
Some directories are setup to allow webmasters to trade links instantly with the directory itself. (This is commonly know as a reciprocal link directory.)
Some directories are often added to a website, using a sub-directory or sub-domain.
Directories can serve many different purposes, depending on who you are and what you are trying to achieve.
From what i have learned is that if google or some search engine sees too many links going out of your website, it doesn't look good, so with sites that have many many links (over 30ish), then for some of them, they would make them do not follow, so the search engine doesn't count them. At least this is how I understand it and how it works.
When you obtain nofollow links from the appropriate category and also from most appropriate sites then it helps you to increase your website relevancy which is very important for your site as well as it is helpful to increase traffic otherwise Google does not give any significance to nofollow links to increase your PR or website ranking on search engine result page.