In a previous post, 1,000's of Files to Rename - 1 Easy Solution, I recommended the file renamer - Denis Kozlov's ReNamer.
At first glance, there's one feature that's missing - the ability to rename folders.
Well, it IS there. You just have to dig a little to turn the option on. In the divider, between where you drag the rules and the files, you'll see some drop down menus. Choose Filters and check on Add folders as files. You'll notice that you can now drag folders into the files area and have ReNamer's rules apply their changes on the folders, too.
Additionally, there is another free renaming tool you can use if ReNamer doesn't do it for ya' - LupasRename. It's a favorite at work and for good reason. Give it a try!