Site architecture and SEO are important when building or designing large sites. Specifically, Google guidelines suggest that no more than 100 links feed off of each page (more for larger sites). Also, the site architecture needs to make it clear what page is related to what, needs to be easily spidered and of course, support the user experience.
In my own experience, a 3-tier flat site architecture is ideal, with the 4th tier for very long tail related content when used at alol. This combined with relevant cross linking can help pass the appropriate level of link juice from page to page.
Here's a great video from SEO Moz that reviews the concept os site architecture and SEO.
SEOmoz Whiteboard Friday - Flat Site Architecture from Scott Willoughby on Vimeo.


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