Some Random Ideas
If it takes more than half a second to react then people will get frustrated and lose interest. The system must be always poised for input. When using the pen, the recogniser should anticipate the input by the type of field and have the appropriate keyboard standing by. Use gestures to launch functions and shortcuts based on short non-existent words to enter long strings of common text. An example would be writing hh to enter http://www. or cm to enter .com.
Grabbing an object and starting to drag then pausing could cause a list of logical targets to pop up next to the object.
Tapping the title of the timeline would pop up all of the object categories. Tapping the name of an object would show a view with only that object. Checking a name would add that object to the default view.
A services area for printing, backing up, burning to optical disc etc with targets that would be dimmed if the actual devices weren't connected to that particular host. The object could still be dropped, but it would be pending.
Printing paper with labels would have two dimensional barcode that would be similtaneously scanned and re-written by the printer. This would keep track of how many labels were used on the sheet.
The desktop device could include the ability to be always running and acting as a gateway for the PDA in wireless mode. Bob could walk around the house and get mail and news and make phonecalls. Those calls could use the landline. He could use that link to control the entertainment system. The entertainment hardware could be shown in the database panel or as part of a row of buttons that could include other attached hardware.