Most people seem to use the third-party app GoodReader or PrintCentral. These allow you to wirelessly transfer files and folders between your PC and iPad. I use PrintCentral (it also supports in-app printing to non AirPrint printers). You can simply select any file(s) or folder(s) and transfer them in either direction.
Another option is to use Apple's cloud server MobileMe iDisk app. This allows you to transfer any file from your PC to the iDisk and then download the file to the iPad using iDisk app on the iPad. The advantage of this approach is that, if space on your iPad is at a premium, files are stored off the iPad and only downloaded - via WiFi or 3G - as needed. Many apps support in-app import and export using iDisk directly, so it can be more convenient.
Tim
Scotland