Article directories have been a great source of back-links and visibility. Am writing this article as am running an article directory myself for the last few years, and I do feel that this section of the web needs lots of improvement. The following tips will not only help the article directories but also it will help the article submitters.
1) Technorati Indexed: Get your directories indexed and claimed at Technorati, that way people submitting their articles will get Technorati votes and authority.
2) Do you accept those articles with links inside the article, this might be a risk, as Google might find this as a paid post and give your article directory a penalty. Even if its not your fault as the article if free so no paid links stuff but you still dont want to get penalty due to poor and in-efficient googles algo.
3) Is your site properly cashed? Check your last 50, 100 or 200 article, and see if they are even indexed by Google or not. When was the last time Google bot gave your site a visit. This problem is mainly because article directories dont add unique content, so search engines dont find anything useful in these sites and stop visiting frequently....