Google and Bing have both talked about site architecture issues lately on their blogs. Site architecture is an important part of search engine optimization, and crucial to ranking.
"You can have great content and a plethora of high quality inbound links from authority sites, but if your site’s structure is flawed or broken, then it will still not achieve the optimal page rank you desire from search engines," says Rick DeJarnette of Bing Webmaster Center.
If you have time, and site architecture is not your strong suit, I would suggest reading both Microsoft's post and Google's, but to sum them up, here a few tips from each of them.
1. Use descriptive file and directory names
2. Limit directory depth
3. Limit physical page file size
5. Use 301 redirects for moved pages
7. Implement custom 404 pages
Google starts out by talking about some site architecture myths, and also shares a couple slideshows (they talked about the topic at SMX London).
Finally, they offer these tips:
1. Check that your robots.txt file has the correct status code and isn't returning an error
2. Keep in mind some best practices when moving to a new site and the new "Change of address" feature recently added to Webmaster Tools.
3. Review the settings of the robots.txt file to make sure no pages -- particularly those rewritten and/or dynamic -- are blocked inappropriately.
4. Make good use of the rel="canonical" attribute to reduce the indexing of duplicate content on your domain.
As I said, Google and Microsoft both have plenty more to say on the topic in their respective posts. The Bing post is actually the third installment in a series.