I have iPhone 3GS and I have bought a new iPhone 5, my question is how do I transfer the data as it is with out duplicating it on any of the devices.
I have an registered apple ID sync with my Mac book pro.
The easiest way is probably with iCloud, do you use it? If so, go to Settings > iCloud > Storage & Backup > Back Up Now. Then restore that backup to your iPhone 5. For more details, see here:
|iOS: Backing Up and Restoring Data to a New Device|