Extraordinary long backups are caused by an error when an app (or apps) was installed or updated, particularly if you have ever installed or updated using the App Store on the device itself rather than iTunes. Even if you were never aware that there was a problem, they can arise and will cause problems with the backup process. Maybe you did have a problem during an update or install. Maybe the update stalled, or the App Store crashed. These issues are very likely what have been causing your long backups and you didn't even know it. During the backup process these errors cause it to drag and pause for a very long time before it gets moving again. From your view, you just see a normal backup that is taking hours, and undoubtedly annoying you to no end. On the inside, iTunes is trying desperately to get past a roadblock that it doesn't know where it came from.
This is how to fix the problem. This is not a quick fix, but it is an effective fix. And it is a FIX, not a band aid. Depending on how many apps you have installed, this can take several hours to complete. You will also lose all game scores and any other data stored in your apps. You will be starting fresh. It is an inconvenience, but in the end, you will be rewarded with quick, efficient backups, the way Apple intended. And you will never have to dread the iTunes backup again.
1. Open iTunes, go to Edit>Preferences>Syncing and remove all previous backups. Also click "Disable automatic syncing for all iPhones and iPods"
2. In your system file structure, locate the backup files for iTunes.
On Windows: C:\Documents and Settings\USERNAME\Application Data\Apple Computer\MobileSync\Backup
On a Mac: Users/YOURACCOUNT/Library/Application Support/MobileSync/Backup
Delete ALL files and folders inside the Backup folder.
3. Plug in iPod. On the Applications tab, uncheck sync apps. iTunes will ask if you want to remove the apps from the iPod, say yes. Click sync. This will remove all apps on your iPod, it will also backup the ipod. This backup will be very fast, and will recreate the backup folders you deleted in step 2.
4. After the sync is complete, if there are any apps left on your ipod, touch and hold the icon until it starts to wiggle, then touch the X to delete the app. Delete all apps left on your ipod. Then sync again.
5. After the sync is complete, disconnect the iPod and do a hard restart by holding down the sleep/power button until the slider appears, slide to power off. Wait 5 seconds and push the power button again and wait for the ipod to boot up.
6. Connect your iPod again. Now begin adding apps back to your ipod one by one. On the Applications tab, click "Sync applications" AND "Selected applications". Make sure all apps are unchecked.
7. Check one app and sync. After the sync is complete, right click on your ipod under Devices in the left column of iTunes. Click "Back Up" and allow the backup to complete.
8. Repeat step 7 for each app you want to install. Keep the previous installed apps checked, just check one more app each time. Be sure to backup after each install. As you add more and more apps, the backup will take longer and longer as the process scans apps for changes. An initial backup can also be long for a particularly large application. However, ONLY the initial backup after you install an app will take a long time. Subsequent backups are very quick. Even these "long" backups are just minutes long, sometimes up to 15 minutes in my experience.
9. When you are finished installing and backing up all apps, go to Edit>Preferences>Syncing and enable automatic syncing for all iPhones and iPods.
10. Unplug and plug your device back in just for kicks. Let it back up and sync. Better?
The very first time an application is backed up, all critical data is written to your hard drive. This is why the backups are so long the first time. Afterward, only data changes are written, so backups are much shorter.
Backup times will continue to vary based on how many apps were altered since the last sync. If you've used one app since the last backup, your backup will be very short. If you've used 20 apps, the backup will be longer. But you will be rid of the dreaded hour (or more) long backup, that is a promise.
Now that your apps are installed and backing up correctly, the number one rule is to never, ever install or update apps through the App Store on the iPod. ONLY install and update through iTunes, and backup after every install or update. The App Store on the iPod is still unstable and can cause lock ups, crashes and freezes. And it is the culprit in these long backup times. Avoid it until the bugs are ironed out.
Also, do not be tempted to disable backups using programs or code edits available online. Your backups are crucial in the event of a restore. Backups contain all of your personal data like game scores, notes, icon arrangement, application data, etc. And it's not a matter of if you'll have to restore one day, it's when, and you'll be glad you have a backup when you do.