The data is stored on your Ipod Touch, not iTunes. The app resides on iTunes without data pertaining to whatever you did you the particular device. It would be nice to transfer it all from one to the other but I doubt that's going to happen any time soon.
you are wrong the data is also stored in iTunes, i restore my 3Gs some days ago and all the data be back and work as a charm
Umm not really,the apps are stored in iTunes but the backup holds everything including the settings and inapp data,now if you want to carry off your data from the apps say from iPhone 4 to iPad then you will have to restore from the iPhone 4 backup,simple sync is like installing new apps and copying off certain independent files such as music video photos but the inapp data such as login info and settings of tweekdeck for instance From iPhone or iPod can only be copied exactly to iPad by first taking a backup of iPod/iPhone and then restoring that backup into an iPad with tweetdeck,now once done you'll find exact settings and username/password used in iPhone/iPod is also exactly there in the iPad. But remember that such restore often cause instability and data loss too,so look before you leap and don't cry later.
iPad 3G (32GB)
iOS 4.3 iPad - The awesome tablet that matters