It may be natural flow, depending on the relationship of the content at example page to both Parent Pages.

I am guessing that when you get to Parent 1> there are more pages linked to there than example page (otherwise, that is some pretty bad hierarchy). The same for Parent 2> : example page is related to both Parent pages and visitors may want to get to example page for the related content from either page, then it is natural.

Realizing that most sites' home page is not always the point of entry for visitors it might be better to link only to the Parent n> pages from the main page. Because you understand the relationships between these Parent and Child pages better than others, you can probably determine which are your most popular pages and where visitors navigate from those pages and how often visitors skip the parent page to go directly to a child page. If that never happens, you may be better to link to 'example page' only from those Parent pages and leave it off your main page.

This isn't any specific suggestion, but some things to look at to see why and how to offer better navigation. Generally it is a bad idea to link to all pages from the main page - and obviously there is a big difference between a 25 page blog about "My favorite Widgets" and a 25,000 page site about "The History of Widget Design and Development Since the 12th Century". Point being- think of your users, how they use your site and cut back on unnecessary internal links that don't have a reason to be included. Fewer internal links is usually beneficial to any site, as long as it helps users find content quickly.

Yes, there are many more pages linked from Parent 1 and Parent 2.

Would it make sense to have duplicates of each of those example pages under each parent. Same content, different page and different path and then canonical to the page that we want indexed? Or have 1 page and create dynamic breadcrumb navigation that follows the users path?

This is where I'm really struggling.

In that case I would "have 1 page and create dynamic breadcrumb navigation that follows the users path" - as long as the navigation can be generated even when the user enters on that "sample page".

Pages can have more than one breadcrumb trail. For example:

Books › Authors › Stephen King
Books › Fiction › Horror

[support.google.com...]

Thanks for the feedback. Even more clarity from Matt Cutts:

[searchenginewatch.com...]

Sounds like everybody is assuming that navigation structure and url hierarchical folder structure are the same. This isn't necessarily the case.

Well, that's kind of the reason for my question in the first place, right? My folder structure and navigation structure are not the same and I'm trying to find ways to compensate for that.

Take a look at this discussion, and in particular g1smd's comments on faceted navigation....

Matt Cutts Interviewed by Eric Enge
http://www.webmasterworld.com/google/4097582.htm [webmasterworld.com]

As g1smd notes....

The multi-faceted hierarchy does not need to be included in the URL of the individual product pages.

A CMS that automatically includes the hierarchy in the URL is likely to be a problem.

Wow, this is a very interesting perspective and something that I had not considered.

brandozz - I'm glad that this perspective resonates.

It may be difficult, though, to apply to an existing setup, and I've seen attempts to do this break in some CMSs (am thinking of one particularly that was built on IIS).

This isn't my area, so I can be of only limited help, but maybe we can get others to join the discussion if it gets that far. What kind of CMS are you using?

I'm going to be using WordPress.

WordPress is notorious for having multiple URLs for the same content. This helps when it comes to organization and searches, but for indexing, not so much. I use a plugin to control the indexed taxonomy of posts and pages. You can also set a canonical preference.

It is important when you first set up your WP permalink settings to choose the taxonomy you want to use, and use a SEO plugin like Yoast's to take care of sitemaps, indexing options and canonical settings. Changes can be troublesome after you start generating content. I believe that most people use page-name and not /category/, /tags/ or /archives/ but for some sites those might not be the ideal choices.

Wordpress SEO by Yoast is usually one of the first plugins that I install.