It is going to depend upon the application. When you are dealing with an energy source that is essentially constant voltage such as NiMh or NiCd batteries in the end it makes very little difference whether you measure the capacity in watt hours or amp hours, Voltage is almost constant throughout the discharge, so there is a straight line relationship between the two. Once you leave the realm of constant voltage sources (such as LiIon batteries), the picture gets a lot murkier. If the device uses a linear driver, then the measurement will have to be amp hours to be meaningful. If I have a 12 volt 2 Ah supply that feeds a linear driver that outputs 2 volts at 2 amps, no matter what the watt hour capacity is, the run time will be an hour because the linear driver supplies constant current, and simply wastes excess voltage as required. So a 12V 2Ah supply has 24Wh capacity, but gives the same run time as a 2 Volt 2 Ah supply. In this case the Watt hour capacity is almost meaningless because the linear driver is just wastes any voltage in excess of what is required.
Boost and true Buck drivers for example are basically constant wattage output devices with a known conversion efficiency. If you need 4 watts output as in my previous example, it is going to take something a little in excess of 4 watts input regardless of the supplied voltage. So a fully charged LiIon is going to need to take about a amp at 4.2 volts, however when the battery has been run down to say 3.2 volts, that same driver will draw about 1.25 amps. If we carry it even further and compare the difference between a driver fed with a pair of CR123A's in series versus a single 18650, our 4 watts will need about 1 amp from the 18650, but only about 670 mA from the pair of CR123's. Having said that, the conversion efficiency does tend to decline with failing supply voltage. I.E. The efficiency of the driver is likely to be higher with the pair of CR123A's than it will be with the single 18650.
In the first case, mAh and mWh will give you the same answer, in the 2nd case, mAh will tend to overstate the useful capacity, and in the 3rd case, mAh will grossly understate the capacity for the CR123 based supply compared to the LiIon.