What tools allow a quick comparison of NetCDF output from ocean models?
For very quick visual comparison I would use Cube Browser or ncview together with a command line tool like the Climate Data Operators. For quick production of nice looking graphics (and animations) Panoply really makes good job. For further analysis or special graphics keep following your approach and script with things like MATLAB, Python (e.g. with Iris), IDL, R, ncl or whatever people around you are using.