The present invention provides an optical amplifier pre-emphasis and equalization method that alleviates the optical amplifier gain ripple penalty experienced in conventional optical communications systems. This method includes storing measured communications channel signal gain ripple information, acquired during factory calibration, in the internal memory of each optical amplifier module. When the optical amplifiers are assembled into a chain, system software retrieves this communications channel signal gain ripple information from each optical amplifier module and computes the pre-emphasis or equalization required for each channel in order to obtain a flat SNR at a receiver. The method also includes measuring the ambient temperature of each optical amplifier module and applying a correction based on the expected change in gain response of each optical amplifier. The method further includes, for Raman amplifiers and the like, applying a fiber type, gain setting, GFF error, etc. correction based on the expected change in gain response of each optical amplifier. The method relies on using VOAs at the sources or DGEs/RBFs in the optical signal path to pre-emphasize or equalize the optical channels.