As buZz says, you won't be able to hook the arduino up over USB to most pocketPCs, as they can only do the 'little end' of the connection.
Many PPC devices have a serial port in addition to their USB sync port. If you can get a serial sync cable for your PPC then you could talk RS-232 to an arduino's serial-port. If you had an older serial arduino board, it would work right out of the box, as these boards are intended for RS-232 voltage levels.
If you have a USB board or the moderndevice.com barebones serial board, you'll probably need a level-shifter (max-232 or similar) to convert from the +12/-12 votages of RS-232 to the 5v/0v "TTL serial" on the microcontroller end.
If the PPC device is robust enough to accept 5v/0v input levels, you could possibly bodge up a simple level shifter using zener diodes, like the one used in some serial-port avr programmers: http://www.lancos.com/e2p/siprog_base.png
I've got an old iPaq 3600 lying around somewhere, but no serial cable for it. Another option might be a compact-flash serial adaptor.