This used to be easy to do with a .gtkrc-2.0 in Ubuntu 11.04 and previous releases. I am using a third-party theme (Elements) and I really like it, but the Nautilus sidebar is ugly and dark and I want it to match the rest of the theme a little better.
You would need to edit the css themes for the GTK+ 3 theme to accomplish this. You can use other themes (there many themes on gnomelook.org for you to look at).