After much discussion with people who had their site banned recently, I'm of the opinion that the penalty stems from "common linking". Here are some of the symptoms that I believe may have been the cause:
1) Link exchange programs that involve all sites on a network. For example, someone starts sending out emails requesting link exchanges with their entire network of sites, so the result is that everywhere you see an incoming link, you also see incoming links to other sites on their network.
2) Directories as sole source of links. There have been people who put up sites, and since they don't want to do link exchanges, they seek one way links through directories. In addition, they submit multiple sites in this manner, and also do some interlinking between their sites. Once again we have a network of sites with links that come from a common source (directories, often the same ones).
I think that if you are going to run programs to increase backlinks to sites, you need to:
1) Run a separate program for each site
2) Be careful not to use the same tactics for each site. For example, don't put all of your sites in a coop program (but don't be afraid to use coop for a couple of them).
3) Make sure sites on your network are getting their links from unique sources. Don't get lazy and keep using the same list of sites or directories.
4) Do not submit only to directories, but also find sites that are of similar interest for link exchanges (if possible).
5) For each site, vary your methods: link exchange, coop, article submissions, press releases, signature in forums, directory submission, linking within your own network. So don't do any of these too much, but do a little of each.