I've also heard the same thing about footer links being ignored, however, I have seen the opposite many times over.
As an example, I recently saw a fairly brand new site rank very well - its backlinks were composed of a footer link on every page of a totally unrelated site (assuming paid link as it was different owner) and a link network setup within its own other sites - that was it - period.
And, now that I think about it I did some domain cleaning myself not too long ago. I'm talking sites I haven't looked at in years. Well, one in particular I had used done this same thing we are talking about (I think most everyone did back in the day as it sped up the process of showing up)... well, removing the links and what not caused its pr to drop almost immediately. In this case I could have cared less as I didn't use or look at the site, but it backs up this point.