Dolby Digital has actually made the situation worse. Programs authored in Dolby Digital have a way to tell the audio system what level dialog should be reproduced at (relative to maximum level). Many commercials do not use Dolby Digital audio and therefore has no dialog normalization and the audio system goes to a high gain setting. Dialog normalization can also be authored incorrectly.
Hopper/Joey have a mechanism called "Volume Leveling" (in Audio Settings menu) that is supposed to level program/commercial differences but only works on PCM (non Dolby Digital) audio. I have not played with it but it does seem to bring hot PCM audio down in level so may help match DD and PCM audio.
werdztif85 suggests selecting PCM Only for audio output. This will prevent Dolby Digital audio from reaching your audio system so it's not recommended unless you only have one-two speakers. This selection does not seem to affect HDMI audio.