You should use the Yoast Robots extension to fix almost all the duplicate content.
http://www.magentocommerce.com/magento-connect/yoast-metarobots.html
When using 2.0 Magento connect: http://connect20.magentocommerce.com/community/Yoast_MetaRobots
for 1.0 use: magento-community/Yoast_MetaRobots
Also use canonical URL. You can find this at the admin panel:
System - Configuration - Catalog - Canonical links for catagories
System - Configuration - Catalog - Canonical links for products
