A charger would have little effect on a new battery like the ones in our phones. Charging speed does not normally affect current drain on lithium ion batteries like the one in the device. I've had different results after running a lot of programs, and just after a reboot. It all depends on how fast the phone draws current from the battery.
Different voltages would have an adverse affect that you'd see, in that the phone would not charge. USB charging is meant to pull 5 volts from the pc/wall charger/car charger/whatever and as much current as is allowed. A lower voltage would cause the phone to not see that it's hooked into a charger.
PC USB ports are usually limited to 500mA per port, while the wall charger may allow up to 1000mA. This would explain why PC charging might take longer than with a wall charger.
Either way, once the battery is charged to 100%, however you choose to do it, the longevity of the battery depends on the current drain and the battery's capacity. As people have mentioned, the phones may have different calibration points, making it difficult to compare things like percentages of charge between devices. The only scientific way to test would be to have two phones running the same apps, booted at the same time and used the exact same way, only charged with different chargers.
I guess what i'm saying is that it shouldn't make a difference.