freejung - 9:32 pm on Jun 21, 2011 (gmt 0)
I'd still like to know whether, all else equal, a deeper link will rank lower than one that's higher up in a site's link structure
That's an interesting site architecture question, but probably not directly related to Panda.
tedster is particularly expert in this and perhaps he could comment -- my answer to the question as phrased would be "yes" but with the caveat that if you make your entire structure shallower, that's not "all else equal."
That is to say, if you simply move a single page up one rung in the hierarchy without changing anything else, normally you would expect that page to rank higher, simply because it gets more raw PR.
However, if you make the entire site shallower, in particular if you link to everything from the homepage, you're splitting your top-level PR among many more pages, which will decrease the ranking of the pages that were previously top-level.
It's a fine balancing act -- you want it flat enough that PR gets spread around nicely, but deep enough that the main topics get significantly more PR than the minor topics.
My advice, for what it's worth, is that if your basic architecture was working well for you pre-Panda, don't change it. Focus rather on beefing up the pages you have, that's what seems to have worked best for others.
Anyway, that's what I'm going with. I'm definitely not going to link to all of my bottom-level subcategories from the homepage, that would be a horrible mess.