Advantages of Isolated DC-DC Converter over non-isolated?
If you have high currents or frequencies riding around one part of a circuit that you'd like to protect another part of the circuit from, isolation is certainly an option.  For example, if you have a microcontroller driving a high-current motor with PWM, you can optoisolate the PWM pin on the microcontroller, then power up the motor circuit with an isolated DC to DC.  Doesn't work if you don't optoisolate (or isolate in some other way), obviously.

If you're building a medical device with patient leads, isolation of the patient leads  might be critical to meeting safety standards.  An isolated DC to DC, along with isolation of all the analog and digital signals that need to connect to the patient would be in order. 

Note that an isolated DC to DC becomes a nonisolated DC to DC if you connect the grounds!!  Also, if you're putting test points into your board, be sure to include one for every ground, and don't forget that its not hard to connect isolated grounds with your oscilloscope ground clips accidentally!