5.00v is ideal, sometimes you run into power hungry boards that require more amps(current) and the only way to give it more current is to up the voltage. If you need to do that you need to check the voltage at the board on the farthest point from the power inlet. If you run a full Naomi setup, sometimes the voltage needs to be upped to 5.6v just so that the entire system is at the 5.00v level. This is why it's good to have both a jamma voltmeter AND a digital multimeter.
But general rule for majority boards is 5.00v and don't go higher than 5.2v as some chips fry at 5.25v.