A reliable way would be to cycle the battery and measure the energy it can store. This could be done by comparing the duration of a battery in good condition under intense and constant load. There are apps like this one, that serve for that. Once you have the duration of the type battery, you can compare other batteries.
If you want to build yourself an invention, with a multimeter and a resistor, it could be worth it. You would have to measure how long it takes for the battery to discharge and take voltage or current points from time to time. With that and some simple calculations using Ohm's law, you can find out the percentage of charge left in the battery.
If you want to automate the process, a cheap way would be with Arduino, which would also allow you to check multiple batteries simultaneously. If the battery is less than 5V (unless you are going to check laptop batteries, that would be the case), you can connect it directly to an analog input of the microcontroller. If you are going to use batteries of higher voltage, you can use a voltage divider (once again, Ohm's law is your friend). You put a resistor and write a program that periodically measures the voltage. Knowing the value of the resistor, the voltage over time and total discharge time, you can find both the total charge (Ah) and the total energy (Wh) and that value you can compare directly with the battery specifications. The calculation can be done in the Arduino programming and returned through the serial port.
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