From the slicer point of view, I find it useful if the layer tree contains a part for the general look of the website (header and such) and then per page a layer tree. That way it's pretty clear which parts you intend to be consistent across the website, and which things are page-unique.
Since not all pages are equally long, the footer doesn't work that way, but if you want the footer to be the same across the website, it could be enough to just put it on the front page and name it as such. That'd be clear enough for me, but I suppose it depends on who's taking the PSD to build the HTML out of it and how much you get to instruct them.
