Hi,
I am quite familiar with Magento and struggling with the SEO of this ecommerce mammoth!
As far as I am aware, you should implement the meta tag "NOINDEX, FOLLOW" on those pages that you do not want indexed - as your pages are already in the index, this is the way to go - blocking them on robots.txt does not get pages out from the index if they are already in there.
I suggest you apply some "querystring" logic to your template - you will find the page here:
app/design/frontend/default/YOURTEMPLATE/template/page/html/head.phtml
That way, you can apply the
depending on the page content.
Hope this helps you and let's stay in touch about Magento! (PM me)