This link removal business adds another cost to what is already only a marginally profitable type of website in terms of effort versus returns. Like Wheel I have an old directory hanging around not doing very much, and the listings are useful if not comprehensive. I've had a couple of misguided link removal requests; there's nothing on the site that would make a human reader think it's FFA or unedited.
What Penguin encourages me to do is to link out less widely, and far less to people I don't know and I'm not likely to have dealings with (at conferences, through personal emails, by blogging about them, or whatever). That applies to all kinds of websites, not just directories. I can't be doing with strangers contacting me and saying, effectively, my site isn't good enough to link out to them.
It takes time to deal with removal requests, whether or not you take down the link.