I'm using a free script for the first time, because I don't have time to code one for myself right now. I'm just waiting for the site to be indexed, but one thing struck me. The script I'm using is the one from http://www.freephpdirectoryscript.com/ It's missing a few features I'd like so I'll probably write one myself in the fullness of time, but do you think the Google algo will look for the copyright link to penalise the page for using a script associated with lots of other sites too?
They do not penalise a site if it is using the same script. However, if you have the same content as any of the other sites using the script, then you would be subject to duplicate content penalty. It is in the google guidelines about affiliates, to make sure that enough different content is provided to distinguish you from the rest of the affiliates. So in the case of using a free script, ensure that you have it unique or with sufficient different content.