iTunes might be a big bag of digital poo, but it’s still disappointing and worrying to hear from One FPS that half of users never sync their devices after the initial set-up:

A little birdie says that about 50 percent of Apple Store customers who need to get their iPhones swapped have never plugged them into iTunes after the initial activation and sync. This is a big reason, according to this birdie, for why Apple Store Geniuses are excited about iCloud.

I’ll bet.

My advice (at least until iOS 5 rolls around): if you don’t care about your iOS data at all, don’t back it up. But if you do care about your data, you should regularly sync your device with iTunes. And if you really care about your data, make regular manual copies of  ~/Library/Application Support/MobileSync/Backup/ on the Mac, \Users\(username)\AppData\Roaming\Apple Computer\MobileSync\Backup\ on Windows 7 or \Documents and Settings\(username)\Application Data\Apple Computer\MobileSync\Backup\ on Windows XP. That way if you do a sync and iTunes screws it up, you still have a copy of your app data stored somewhere safe.

Note that it’s also currently possible to make back-ups of a single application’s data (which isn’t possible to extract from the Apple back-ups) by directly pulling /Documents and /Library folders from an app’s bundle. My tool of choice for this is PhoneView for Mac, but iPhone Explorer will do much the same for Mac and Windows, albeit in clunkier fashion from a browsing standpoint.