When I synced my Ipod Touch 2g to my computer today it took off over 50 apps. Now most of my games data are gone and I have to start them over and reorganize. What happened?
Did you sync it to a different computer? Personally, I'd restore from your last backup (if you've retained an older backup) I've had this happen with my music, as I sync at work and at home (and don't have my music stored at work.
iTunes backs up automatically during each sync. I notice that if I delete an app and sync with itunes, then redownload the app from my iPod, then during the next sync the app gets deleted.
This is why I have automatic syncing disabled. Also, if you've gotten apps from a different computer, or from the iTunes store it should ask you if you want to copy that content, if you say no, it will get deleted. There is an option in iTunes to transfer purchases from your device.