A footprint is something that is common among a group of sites. It could be image names, pubid (adsense), code patterns, comments, content links (powered by somedomain.com) etc. So if you use the exact same website template for each of your sites, humans or bots could look for a common identifier and either exploit it or penalize you for it. This is really important when you are mass producing sites with tools like YACG.
To avoid footprints, try to make your sites as original as possible.