Jalinder - 3:27 pm on Feb 12, 2005 (gmt 0)

How about having all directories as only first level by using URL rewrite?
On the server real directories will not exist. A common file can be used and with help of some URL rewrite software, the directories will display as:
domain.com/animals
domain.com/pets
domain.com/dogs
domain.com/dog-health
domain.com/dog-medication
domain.com/cats
domain.com/cat-health

Linking can be animals -> pets -> dogs -> dog-health -> dog-medication
and animals -> pets -> cats -> cat-health -> cat-medication

Later on if a change in structure/theme/linking is required, like adding pet-health because dogs and cats are not working, a new category domain.com/pet-health can be added. Links will then change to:
animals -> pets -> pet-health -> dog-health -> dog-medication
animals -> pets -> pet-health -> cat-health -> cat-medication

The site gets independent of the directory structure this way and can change links/theme later if required. For user it will be easier to type any URL if most are first level. They might get habitual to this and start typing any keyword .. almost like search! For people who want to link to the site, a simple url is always good. In SERPs a first level directory highlights the importance your site is giving to that term, savvy people like us do take a look at url if it is simple and when it exactly matches our search term.

Of course where applicable a 2nd/3rd level sub directory will be used when it perfectly fits. E.g.
domain.com/dog-health/dog-health-questions
domain.com/dog-health/dog-health-advice

Overall everything (directory wise) will stay within 3 levels however big the site is. Linking may go deeper, but its always in your control and you can change it as your content grows (also as your knowledge of SEO evolves).

Only thing is search engines might frown how you can have say 3,000 first level directories!