Matt cuts has made it clear that he doesn't consider all web directories to be "crappy"... And I still see the ones that fit his criteria as having value, but the multitude of me-too spammy directories are IMO useless.
As for the OPs question... I'm not seeing any value in bothering to get a ton of crappy links from Russian porn sites and the like. Even if it doesn't hurt you it's unlikely to be worth doing.
I also had a directory back in the heyday of directories, but I converted it to another site few years ago after Google went on its vendetta against low-quality directories and paid links. I would have to say that my directory was low quality because it was a mix of free and paid links with simple listings and no business profile pages. I tried deep linking and had several thousand links (mostly from other crappy directories) pointed to it, but the traffic (other than spiders) dropped off to near zero.
Originally Posted by bogart
I suspect that G does not stop crawling a site, even if they have flagged it. The real question is whether or not the links have any value. With a grayed out PR on a page, the links are not passing any PageRank and are probably not showing up in Yahoo as backlinks. Those signals from two different search engines tell me something.
There are some good directories. It appears to be a matter of having high trust value because they confirm a physical street address for a business, include a business profile, and allow users to rate the businesses. I scan through Places accounts and keep a list of the business directories that Google automatically associates with Places accounts. Here are some of the most popular in the USA: Kudzu, Judy's Book, Dex Knows, Super Pages, Yellow Bot, Yellow Pages and Yelp. There are probably 20 to 25 directories that consistently show up in Places.
I think that the grayed out pages from the free directories are in the supplemental index. I agree with you that the value is minimal or non existent. I never see any of the free directories is the results anymore. But the local directories show up all the time.