You should take a look at what Matt Cutts says about directories
To paraphrase some of what Matt says in the video:
When looking at directories how does google assess if they are useful to users?
What is their editorial policy? Do they go out and find good links that would be useful to users? Do they review sites and reject sites that are of low quality? Typically paid links are going to be much more low quality or somewhat automated, and accept any anchor text. And if you make a great site you don't have to go out and submit your site to a thousand directories.
In another video Matt says that they don't punish sites because of the CMS they are running. It is quality of the site that matters. I wrote a little bit about quality guidelines for directories on the phpLD site.
My advice to you is that if you are going to start a directory, make sure you have some goals in mind to insure you are going to create a quality resource, and you should be fine. Plan on adding useful links and content yourself. Don't just wait for links to come to you. Don't accept any site willing to pay you for a review. Instead, actually review the sites carefully. See yourself as a user visiting your directory and ask yourself what makes it a useful site. Find ways to make your site worthwhile to click through the links.
There are well over 100,000 directories on running phpLD of all different shapes and sizes. There are niche directories, general directories, and local directories. Some sites running phpLD don't even look like a directory. They are masterpieces in a unique way. There many with high pagerank both on internal and external pages.
I think the same could be said about Wordpress blogs or phpBB forums. There are definitely large numbers of sites running these CMS that don't do well in google, and lack quality such as having duplicate content or being nothing but a place to drop junky links. The nice thing about phpLD is there is a review process and the admin or editor must approve the links and articles that are submitted. Now if the admin does a poor job of this, that in unfortunate. But don't let a few bad examples dissuade you from creating a great resource if that is your passion.