I still disagree that "in the head" is where it belongs.
I do agree that having a script element randomly placed in the body is a pain to find and maintain, and it shouldn't be there. However, I think right before the closing body tag is perfectly acceptable and just as easy to maintain as if it's in the head. And you get a boost in load speed.
Once again, the exception to this is in cases like Stormrider describes where you use JS to heavily change the layout. In these cases I'd put it in the head so you don't get a random rearrange of the screen.
However, things like click events and other things that don't appear initially should be in the footer.