Hi,
They do make battery analyzers/chargers that also make tests and do discharging, but i think they are kind of pricey.
The way i do it is connect my batteries to a special volt meter that connects to the computer, and apply a known resistive load. The resistive load allows you to know the current as well as the voltage by only having to monitor the terminal voltage. The software can then know when the battery is fully run down and also how much current was flowing over the total time it took to discharge, and it therefore can calculate the ampere hour capacity of the cells.
To do this without a special volt meter isnt too hard either, but requires logging values by hand every 10 minutes or so. You would connect a resistive load while monitoring the voltage, and knowing the resistance you therefore know the current, so as you log that every 10 minutes you get a list of values that you then add up and you can calculate the ampere hour capacity of the cell. It's not hard to do either.
Once you know the ampere hour capacity you can then monitor the charge of the cell and estimate the capacity that way too. You have to be able to measure the current for that procedure though, and log those values vs time.
The hardware and software i designed does all this automatically, but as i said you can do it manually and it's still very interesting. I've found many cells that dont live up to their ratings, and some that do. For example, i tested some Kodac low self discharge cells 6 months after they were charged and they did hold their charge pretty well, just as advertised. I did this with a complete discharge test. I did the same with 'regular' cells and found them to be almost discharged or totally discharged after that long. The Eneloops are supposed to be good too, but i havent gotten to test any of those yet.