The Search Engine Theme Pyramid [searchengineworld.com] is a way to make good use of PageRank and Google's liking of link text while being ready for theme based engines, giving users easy to follow navigation and making site maintenance easy.
Example Google Optimised Themed Structure
The example site is about widgets, it is called widget-world.com. The home page receives a lot of good links (and PageRank) because people like the site. Most of these links use the word 'widget' or 'widgets'. We title the home page "Widget World, we have Widgets" to capitalise on those links and their link text; we also use the words widget and widgets in the page. We reinforce this by linking back to the home page from every other page in the site, using the link text "Widget World, we have Widgets".
The next level has the colours of widgets, widget-world.com/blue/ I don't worry about keywords in URLs for Google, but other engines like them. It is titled "Blue Widgets from Widget World"; the body text mentions blue widget and blue widgets; the link text from the home page uses the link text "Blue Widgets" or "Blue Widget Collection"; all other pages in the blue widget section link back with that link text; and if we have a good range, other webmasters may link from their pages about blue widgets.
The next level has types of widgets. The widget-world.com/blue/fuzzy/ page is titled "Fuzzy Blue Widgets from Widget World",; the body text mentions blue fuzzy widget and blue fuzzy widgets; the link text from the home page uses the link text "Blue Fuzzy Widgets" or "Blue Fuzzy Widget Collection"; all other pages in the blue fuzzy widget section link back with that link text, and if we have a good collection, other webmasters may link from their pages about blue fuzzy widgets.
Below this level could be sizes, or whatever depending on the size of the site.
Rationale: As the terms widget and widgets have the most competition in the area, we are targeting the title, body text and inbound link text on those words in the highest PR page. As the colours of widgets have significant competition in the area, we are targeting the title, body text and inbound link text on those words in the next highest PR pages. As the fuzziness of widgets has a little competition in the area, we are targeting the title, body text and inbound link text on those words in the medium PR pages. As the sizes of widgets have almost no competition, we are targeting the title, body text and inbound link text on those words in the lowest PR pages. If we don't rank well enough, we need more inbound links.
Keep Important Phrases High in the Pyramid. The pyramid structure dilutes PageRank with each link, but we get to pick which pages get more than their share of PageRank. The decision to use /blue/fuzzy/large/, /blue/large/fuzzy/, /large/blue/fuzzy/, /large/fuzzy/blue/, /fuzzy/blue/large/ or /fuzzy/large/blue/ depends on the competition for the words (do more people search for blue widgets, large widgets or fuzzy widgets?) and on the mindset of potential customers (hopefully both considerations lead to the same choices). Also, Google likes matching phrases, so if more people search for "fuzzy blue widgets" than "fuzzy blue widget" then we should use "Fuzzy Blue Widgets from Widget World", not "Fuzzy Blue Widget Collection from World of Widgets".
Some people would put the second level (blue in this example) on separate domains or sub domains. Unless this can get us more directory listings or other links than we would get on one domain, it will not help in Google. If the linking is just hierarchical (the colour pages link to and are linked from the central domain, but not each other) then it shouldn't matter (hub and spoke relationships seem OK), but if the domains link to each other then there's potential for a penalty (do a site-search for PR0 for more information).
Customising the Pyramid: There are times when the pyramid needs to be adjusted. For example, a highly popular (or high margin) product might want to be linked from the home page as a 'featured product'. This will hopefully help more people to find it easily once they’re in the site, but it will also boost those pages in link based engines such as Google.
Dilemma: We can end up with repetitive phrases in the navigation. It is worth spending time discussing options for naming the navbar/home page links, compromises are generally necessary to help make links descriptive enough for robots to understand, while not bring overly repetitive for human visitors.
Summary: We don't have to choose between themes and Google optimisation. Why not have our cake and eat it?