Yeah, you can add the User and app folders to your backup and if you have a good backup system then you're lucky. Windows' backup will choke on the files and if you're using Norton's backup it'll take you a while before you can specify anything but the default.
I found this backup app for Firefox and Thunderbird when I was upgrading some systems at home.
Once you've installed it be sure to specify a new location for the backed up files.
You can also specify exactly what you want to backup. I'd suggest to go for the whole chabang.
