Of what use would links be, if search engines were unable to notice them? A link received by a website from a directory is considered only if it is possible for the search engines to 'read' or 'detect' that link. If the search engines can read these links, they are SEO-friendly links. The directories from which these links are received are SEO-friendly directories.
There are several factors that make a directory SEO-friendly:
There shouldn't be a META nofollow or noindex tag on the link pages
The links shouldn't have a 'rel=nofollow' tag on them
The links shouldn't be javascript-generated
The links should not re-direct
The URL of the links page should not contain too many parameters