There is no quality difference between .mov or .mp4. All my OS X apps handle both just as well.
The only difference is that .mov time stamp varies based on daylight savings while .mp4 is the same all year round.
So I now use .mp4 which makes renaming the files based on their date easier (I use GraphicConverter for that in YYYY-MMDD-hhmm-ss.mp4 format).
Video time stamp and location data isn't yet as robust and standardized as in .jpg, .cr2, .dng etc image formats where the EXIF time and location works well.