Hello,
There was recently a good article about this in the SEOMoz blog.
This is the article link: http://www.seomoz.org/blog/lifting-a-manual-penalty-given-by-google-personal-experience
Here is a quote from the article:" When developing websites for clients, we always include links in the bottom right footer of the client's website. Usually, this is something along the lines of "Web Design Yorkshire | Pinpoint Designs". These two blocks of text include links to the homepage of our agency's website. When looking at the webmaster guidelines, it's pretty obvious that we should never have been doing this, and most likely the cause of our penalty."
Hopefully this helps answer your question!
Ryan Maas