Ages since I last upgraded firmware on my iPhone4, I have mine setup just how I want it on 4.1 with a lot of tweaks and mods from Cydia as well as theme setup etc. Would a backup in iTunes retain all of this including apps etc? I can imagine not.
1. Backup in iTunes
2. Upgrade and restore from backup
3. Jb
If not, would pkgbackup do what I'm after? If not then I think I won't bother upgrading as not really needed