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Which is better for search engines: external or inline menus? And which language: CSS, Javascript, or both?

On our weekly SEOmoz crawls, we get thousands of warnings about overly dynamic URLs as a result of our product sorting options at the top of our category pages.  It seems like the ability to sort products by price, name, etc., is nice for the customer.  For SEO is this really a problem or can we ignore these warnings?

I carry a line of products that come in 4 sizes and 15 colors.  Is it better to have separate products for each combination (Red Large, Blue Small, etc), or a product for each size with attributes for the color, or something else? Also, should I put the brand name in each product name, or only put it in the category that contains that brand?  Thanks.