Uber25206, using the Transfer Purchases function in iTunes will only transfer the app files and not the app data (such as game-saves that go with it).
I am not quite sure whether iOS backups, store app data though. iOS backups are effectuated for your iOS device either by iTunes (upon iTunes sync) or through the iCloud (depending on your iPhone settings and iOS version). To enable iOS backups via the iCloud, considering you are transferring from your iPhone to your iPod Touch and you are using iOS 5 + on both your iPhone and iPod, go to your iPhone and tap through Settings > iCloud > Storage and Backup. Toggle the iCloud Backup slider to ON. Tap on "Back Up Now" and wait for the process to complete.
Now if you are keen on restoring your iPod Touch from the iOS backup you would need to reset it to factory settings and choose to restore from the backup you have just made. You must ensure before that your iPod Touch is compatible with the iCloud first. It must be running iOS 5 and above.
To check which iOS version your iPod has, go to Settings > General > About.
Here is more about iCloud backups and restoring from an iCloud backup:
http://support.apple.com/kb/HT4859