fathom - 8:10 pm on May 27, 2013 (gmt 0)
I personally think - and my own site's behavior is consistent with but not proof or my only evidence of this - that links are a strong element, but certainly not an exclusive one.
That's why many domains are failing to compete because "WE" have made link development into a completely segregated development.
With Google's algorithm (with PENGUIN as a side dish at the moment) all factors are collectively modeled.
It makes sense that Google started PENGUIN 1.0 on the homepage... it was the easiest place to determine webspam. Ask 1,000,000 website owners to link to you but don't tell them where to link or how to link and you'll get brand based links (company name or URL) to the homepage, what, about 90% of the time.
Tie that into their EMD algorithm and you can fathom "brand based linking" has any enormous advantage... and why when you don't emulate those values... you lose.
Now Google has taken another step deeper into the domain... and brand already had the advantage at the homepage and the homepage tends to feed the rest of the website (unless of course it isn't where the root of your links are coming from.