itunes should done a back up for you. mine did and when i upgraded i restored it and i was good to go all i had to do was fix my mail.app but that always happens to me when i restore my email.
iTunes backs up everything supported by Apple, which includes everything with the stock iPod and the apps, but not apps from Cydia/Installer. Those you have to back up yourself or reinstall them and fiddle with the options again once you've got them all back on. So, only do it if your willing to spend some extra time getting everything up to speed.