One thing to think about when nofollowing, noindexing ecommerce sidebars, which I presume you mean the filters is to have a look at if there is an opportunity to get long tail traffic from those filters. If there is then why not have those filters generate unique URLs that will help receive better organic presence through those long tail keywords?
For example if you visit a clothing store, you will see filters on the navigation differentiated via size, colors, etc. I believe there is potential long tail traffic to gain from this keywords around sizes, colors, makes, brands, etc.
Or check this site's navigation out: http://www.naaptol.com/buy/consumer_electronics/gaming/gaming_media.html
They have used AJAX to avoid creating different URLs (and avoids duplication), and those pages are being indexed, but if you do it this way you are cutting the part where you may be able to get more value from long tail keywords.
Or rel=canonical the URLs
I hope I am on the right path here mate.