We experimentally investigate the real transparency of four-wave mixing (FWM) in semiconductor optical amplifiers to modulation formats involving intensity, phase, and polarization multiplexing. We exploit two different FWM polarization-independent schemes (that make use of two pumps) to wavelength-convert 40 Gb/s single-polarization and 80 Gb/s polarization-multiplexed signals in case of both nonreturn-to-zero ON -OFF keying (NRZ-OOK) and NRZ differential phase-shift keying modulation formats. We found that, although FWM conversion is transparent to modulation formats employing phase and intensity, polarization-multiplexed signals pose serious limitations to all-optical processing transparency.