In the past, the footer of SO-family sites contained links to other League of Justice sites. When Careers was invented, it got added. More recently, a StackApps link got added. And a few days ago, Area 51 joined the club after this question was asked.
The Area 51 link elbowed the How-To Geek's link off of the bar, though, as described here. So what is the rule for which sites get space and which don't? Also, what will determine the content of SE site footers? Will they even be standardized with current SOFU footers? For the moment, this isn't a huge issue, but when Area 51 leaves beta, there will be dozens of official SE sites rushing out of the gates, and I feel that there should be a rule in place.
Obviously, as devinb said, the SO team makes the rule. I'm wondering what their rule is. In the absence of an official post, suggestions are welcome. And yes, I would accept "we change it if and when we feel like it" if it came from a Valued Associate.