Finding EAGLE BOM Parts
Generally for capacitors, any significantly higher voltage rating than the operating voltage will be fine. So you might use a 6.3 or 10V rated part. Bypass capacitors are not very critical as to capacitance value, as long as it exceeds the minimum. You should look at the circuit schematic and try to estimate the actual working voltage. For example, for an RS-232 driver chip powered from 5V you might need some capacitors rated at 16V rather than 6.3V.
If you are redesigning it to use physically smaller capacitors you have to be a bit careful because of voltage coefficients.