Directories which are “paid only” are likely to be penalised with a PageRank drop of one or more points and in more extreme cases a no name penalty. Directories which have free and featured sites would be unlikely to be penalised as long as the featured sites section are shown on the same page as their free equivalents.
My reasoning is that you haven't actually paid for the link but rather the page position. This of course presumes that Google can tell that their are free links on that page. It goes without saying that the site should not mention PageRank at all, no pretty graphs etc, You may also wish to make sure Google believes you maintain a high editorial standard so be careful who you let in and have clear guidelines
I think if you directory has;
- Free Links on category pages
- Featured Links differ only with position and perhaps longer description etc
- Featured Links on the front page are no followed
- Clear Editorial Guidelines
You should be safe but hey I'm not Google so who knows
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