I started my directory with an off-the-shelf script. I seeded it myself from day one with original useful descriptions and reviews. In 4 months the site has made profit everyday. As a result of the most recent updates the site has completely bombed in the SE's. However, in that time I have collected a number of regular registered users that continue to increase my monthly profits. It is not an amazing result but I think it is succesful in its own right especially considering how the majority of new directories do absolutely nothing, ever.
I used an off-the-shelf script for my regional directory, which has now a PR5 home page and some inner pages with varying PR. The WW member who recommended it to me has been PR0'd for his implementation (different region and several years old). We don't advertise this directory as it is primarily for giving links on behalf of customers and we take regional submissions if people find it and submit. It's free for now but could be a paid model eventually. No advertising on it whatsoever. So it is a success, but not a financial one.
My directory has adsense on it from day 1. It has not been clobbered in the slightest, although it did get a bit of a beating over the past couple of updates. It has since recovered and is pulling a little more traffic than it was before. I don't think running contextual ads on any sort of site should would be the cause of any sort of penalty.