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Since Google grades web pages individually I'd optimise each page or group of pages for a specific keyword/phrase i.e.kids clothes, kids toys etc. You can work at getting a no1 ranking for each keyphrase you use.
To accomplish that you need to structure each page so that all the words that are "on the page" and all the words that are "in the anchor text" of the links that point to that page are all within the theme of which ever keywords/phrase you are using.
Work at getting people to link to each specific area of the site using the appropriate keywords in the link text, and just basically target niche directories where customers are going to be looking for your websites products.
Junior
basically there are around 10,000 cats (region based as well!)
scratch what I've just said :)
Another angle might be to optimize all of the categories and the homepage, promote the root really hard, and then distribute the PR and strength to the categories.
You have a task ahead of you with a site size like that!