I left directories business long time ago, some surely remember me. Of course it's nice to see PR back on some sites.. But one doubt: what's advantage of PR for directory if all categories remains PR0? Really I wish you all good luck, but personally I wouldn't be back into directories with what we have now.
It was suggested that the penalisations were for link selling, pr gaming, bad promotional methods and so on. For me personally, it meant 2 of my directories not ranking for their own names, pr removed on all of mine. Now, serps are normal, still without pr though. Length of penalty, over 2 years on one of mine, not sure about the other ones. PR on the last one to lose it happend within the last six months i think, it happend differently for different people. One thing that should be kept in mind is that this doesn't mean that newer directories will not be penalised or that those out of penalisations cannot fall back into another one. It would be wise to tread carefully from now on, although i know thats stating the obvious, but its easy to get excited and fall into the same habits and trap again.
Pipes made a very good answer, I just wanted to add a little further. mid-2007 was actually the year that Google went out on a Trash-out. A couple of my directories (not on my sigs) went out and purchase links on sites that had a greater pagerank, those sites where considered as "Trustworthy" as they say in the SEO business. One of my new bidding directory with a blog had reach a PR5 in such a short time period of the life of that directory, then there was some overzealous people made some concern on Matt Cutts blog about link selling/buying to gain a higher PR and to make it short, the rest is history and so was those two sites of mine and many other directories and "trustworthy" sites. Many of those sites moved on and continued to practice white hat SEO, while others just banished, it was a domino effect. I just want to make it clear here that directories were not the only ones that were penalize by Google. How do we know if we had been penalize? Simple, the tool bar that once say PR5 went to Zero and never regained, no where to be found in the search list or way deep. traffic from the SE had virtually faded away.