@Psy
The reason you might want to keep that backup is that backups that are made in iTunes (when you sync and when you do them yourself) sometimes get corrupted. This way you have a "backup for your backup" kinda thing!

Plus these things are hidden in the deep folder structures of your OS and are usually not named "iPhone backup." However, if you "must delete it" you can google some info as to where they're located and you should be able to turn something up in no time.
Regarding your "post-jb" backups, it is true that your backup saves some jb data; however it's mostly app settings, etc. (such as info about apps you may have put into folders while using Categories, etc. - which is why you want to delete any Categories folders before you restore.)
There's a package in Cydia called AptBackup which creates a "text file" stored on the partition of your phone which does backup in iTunes.
The next time you restore and need to re-jb (fw update for example,) AptBackup is the first thing you download from Cydia after you jb (and restored your iphone backup with iTunes.)
You launch the app and tap the "restore" button and the app tells you to wait a few minutes and it then reads the "text file" from the backup and automatically reinstalls and reconfigures every jb app/theme.
Time-wise "your mileage may vary" (depending of number of Cydia pkgs installed,) but eventually...Voila! Your phone is back to jb with themes applied etc.
I think it's pretty cool!