GoodReader was one of a handful of apps which had figured out how to do USB syncing to iPhones, but their solution was in violation of Apple's iPhone SDK rules. Apple eventually required all 3rd party iPhone apps to remove this functionality. Some apps, like GoodReader, could sync via iTunes but it was very limited. Wi-Fi syncing was also an option, but it was slower and prone to configuration issues.
GoodReader has released a free utility named GoodReaderUSB which, as the name implies to any who haven't suffered a traumatic blow to the head, allows you to connect to GoodReader via USB. The software is free and available for Windows (XP, Vista, and 7) and Mac OS X (10.4, 10.5, and 10.6).
The interface is simple enough, and if you have more than one iDevice you can connect more than one at a time. In my initial testing it worked as expected. The UI is fairly straightforward and allows for drag & drop access, folder creation, and deletion.
GoodReader is available for iPad and iPhone/iPod touch. There's a free "lite" version but the app is easily worth more than the $0.99 asking price. One of the "hidden gems" of GoodReader is that it's not just a reader, but will allow you to download just about any file to your iPhone or iPad by pasting in the URL. I use it for downloading PDFs and then sending them to iBooks on the iPad.