Yeah it can get really confusing.  Here's the concept.  Each Root domain can have many subdomains, as well as sub-folders.

Any link pointing to any subdomain or subfolder will provide some linking value to the entire root.  It's not as much as that individual subdomain or subfolder gets, however the cumulative impact is there and it's real.

The reason is pretty straight forward - any sub, (domain or folder) is naturally associated with the root.  It contributes to the overall weight of that root.

It's not unlike the branches of a tree.  While the rain may fall directly on a branch, some of the water has the ability to work it's way back to the main trunk of the tree.

Just like water that seeps into the ground and soaks into the roots, can and will work it's way up the trunk and to the branches.

It's going to be very difficult for sites to abuse the schema.org structure, though I don't doubt some will try.

And if a site does go that route, it's essentially a deceptive business practice, which may cause them other problems.

If you mean - if we get an inbound link pointing to the subdomain, will the root domain benefit?" the answer is yes to a certain extent.  How much will depend on how closely related the subdomain topical focus is to the root domain, as well as how strong the link is from the perspective of the source site.

If you mean - if we point a link from within a subdomain to a page on the root domain, will the root domain benefit?" Then the answer is also yes, but how much depends on many other factors. And those links will carry less value than most quality inbound links coming from other root sites not in your control.

Submiteaze may include at least some quality directories.  Personally, I've never seen a niche- market high quality directory that allows anything other than direct submission though.

I'm in complete agreement with NinjaMarketer on this one.  Also consider chambers of commerce, other high quality business or industry specific directories, on a case by case basis.  Each one needs to be properly evaluated to ensure the highest quality possible, along with the most relevance - either geographically, or market focused.  There is no "easy" or "quick fix" path to this process if you want to get maximum value.

exactly.  "Tags" and "materials" are not exactly top level category stuff

Etsy's got a good structure with their category and sub-category sidebar that balances SEO and user experience.  note though that when you get deep into the individual Etsy stores, that's gone, because it would dilute the individual store owner's account focus and distract users.

Having all listed and linked is ideal for SEO, however you rapidly cross into usability problems if there are more than a handful. (Would you want 50 or hundred links in a sidebar nav? ) When a site is so big that there are more than a handful that could be linked from that sidebar, it's actually best practice to NOT have any others linked from the sidebar, else you confuse users even more (listing only some, but not all). User Experience is paramount when making these decisions. Even at the expense of SEO in some cases. And if that happens, other tactics need to be employed. Like having a separate, dedicated funnel for "featured properties". Which requires even more unique content in that funnel. But it at least boosts the ranking value for those properties included.

You're dead on accurate in the need for and importance of how "consensus" can help new people get started.  The trick is helping them find enough truly experienced people who have done that testing on a wide enough variety of sites, as well as lots of disclaimers being plainly stated on all such discussions.  It's why I strive to always refer to "in my experience"...

If I have a category California Hotels, sub-category San Francisco Hotels, then having links in a sub-navigation bar to each (if there's only a handful), each of those links reinforces the strength of the top level Hotels, 2nd level California, and third level San Francisco related phrases.  They all support each other.

If, on the other hand, I have a link to "nearby hotels", that implies I'm going from a single hotel details page to a uniquely filtered "geo" category page that shows hotels based on some criteria - it might be all San Francisco, or all within a distance radius, or all within a zip code radius.

Even if it's all other hotels in San Francisco, it's not a link pointing to another (or several) same-level page(s).  It's pointing one layer higher.

That's a filter more than a properly constructed category drill-down.  And it implies that the page I'm on will NOT be listed on that target of the "nearby" link.

just to clarify regarding my input - my perspective is based on my experience with client sites on all scales, small, medium, large and mega sites.

To me it's more important to see how things work on our own sites and evolve them over time as compared to purely looking for what others do or say as it's own reason for taking action.

The slides will be going up at some point in the next few days.  And I'll have a follow-up post that includes the notes for each slide.  In the mean time, I did an article on Search Marketing Wisdom yesterday directly related to the last slide in that deck.

The "nearby hotels to consider" feature is a user thing.  It may or may not pass quality page rank.

In some cases, that extra link could dilute the topical focus / strength of the page it's on.

So if I get to resort X's page, and there's a link to "nearby hotels", there's an implied relationship.  Good for users.  But for SEO, sure it's related stuff, yet maybe not laser focus related.

Another example is blog posts that end with a following box "related articles" and that box contains three or five links to other articles.  Maybe they're highly related, maybe loosely.  If they're loosely related, sure it MIGHT be good to help users.  Yet it probably dilutes this article's topical focus.

Well it depends. Is there only one BMW or are there several? If there is only one, then yes - cross link all the luxury detail pages.  If there are several, then that's the level for cross linking detail pages, even though it's so deep.  If that's the case though, you'd better get inbound links pointing to the parent luxury category page.

And in any regard, don't just have a bunch of links on those category pages - have descriptive paragraph content focused on that category's primary topical focus.

If anything, sometimes silo structure is not the best for user experience, or the drill down too deep, into ever more thinner content to the point where it's so thin as to have a negative impact on SEO and user experience.

I agree with Rand's '09 article in general, however there are some things I think take it a bit too far (such as redirecting PDF documents for link juice).  If a PDF is truly the most relevant content on a topic, I believe it should be indexed.

The biggest factor is that if we get completely bogged down in this process just for SEO sake, we lose focus on user experience.

It's right up there with page and link sculpting - to me, it's a waste of time and harms user experience.  And the time spent going that far is, in my opinion, in 2011 much better spent on other SEO tactics.  Not just because Google has changed how they deal with nofollow links.

Oh - wait I just re-read your question as to not wanting detail pages to link to one another...

If I'm at a sub-category, I would not want, nor need, every individual product/event page in that group to link to each other.  Individual services details pages should cross-link to each other within that service section at that level though, for usability.

Does that make sense? Or did I just confuse you?

Yes - if there are X number of pages within a section, it becomes too many to reasonably link from a sub-nav.  X being a subjective value that needs to be determined case by case.

Ideally, it might lead to yet one more sub-level (such as in sub-sub categories), or in pagination (not blocked from search.  That itself is challenging to do in the right manner so as to avoid going too deep or too thin.

There's no other reason I can think of though, and no other method I'd consider a best practice.

There's never one perfect solution, however here's the bigger issue.  Some people hear "flat" and they take it to the extreme. Which is a terrible concept in 2011.

If you go too flat, you muddy up the proper group relationships.  This is where Siloing comes in.

In my presentation at SMX Advanced this week, one of the many methods I recommend for "sustainable SEO" is to group your content, and reinforce that group relationship in URL structure, then with breadcrumbs, and finally with section-level navigation, where all the pages in that section have a link to all the other pages in that section, but where that specific sub-navigation is replaced or disappears as appropriate when you leave that section.

If you've got more than a handful of pages in a section, you should definitely go deeper.

The trick is knowing how wide, how deep to go.  It's an art as much as a process studying site data over time.

Another factor is the competitive landscape for a particular niche market.  The more competitive, the more important this concept becomes.