iPad File Explorer ($15, free demo with nags) is a Windows application which provides important functionality to your iPad, iPhone, or iPod Touch that's missing from iTunes: the ability to browse the folder structure of the device and easily copy files back and forth. You can even create new folders on your device and use them for mass storage, if you wish.
A couple of caveats here, though. Apple's directories on your device are labyrinthine, and the device also renames everything it stores on the device, relying on internal tags to remember what things are supposed to be called. Luckily, iPad File Explorer comes with preview functionality, letting you test drive most filetypes (such as .MP3) and track down the music file you're missing.
Due to Apple's propensity to rename every file and bury them within folders, iPad File Explorer isn't suitable for backing up your iPad or restoring it. This app's use is getting specific files off your Apple device without dealing with iTunes's esoteric syncing rules, and for creating folders on the device for use as mass storage.
Keep in mind that when using the device as storage, you still won't be able to find the files using Windows. Traditionally, Apple gives you access only to images on your device from Windows Explorer. And if you want to use this program on more than one computer, you'll have to buy another copy of iPad File Explorer and install it at that destination to transfer the stored files from the device to the secondary PC. Still, this makes the gigabytes of storage on your iPad, iPod Touch or iPhone much more useful, and is therefore well worth the $15.
Note: The demo version has a frequent nag screen. The full version costs $15, and it includes a full unlock, free updates, free tech support 7 days a week, and the removal of the frequent nag screen.