Here is a quick fix that worked fine for me on Ubuntu 11.10:
Just put your volume to the minimum and to the maximum value (might need to let some sound play). Did the trick for me.
It seems that something messed up my audio channel levels. In my case the center and LFE (your bass > subwoofer) channel where set to 0 in Alsa. Pulseaudio didn't increase them as I increased the volume. This resulted in having no bass and one channel less while playing normal music (annoying). Also while watching Movies (Surround Sound ones) I couldn't hear what they where saying as that is played mainly over the center channel. So movie music and effects where normal but the characters voices all very dimmed down. Understandably this makes most movies unwatchable.
I did search for this but couldn't find anything recent. I opened up alsamixer on the terminal and saw the channel problem. The solution then was pretty simple. Put the volume to min and max and Pulseaudio and Alsa are synced again. "To max" not on your keyboard as that doesn't go all the way to 11 ;). Open up the sound settings and change it there. You might need to play some sound for this to work. Just use a music player and decrease the volume there as pulse has individual volumes for each app. So you don't annoy your neighbor with too loud music. After that it hopefully should be back to normal again.
I suspect that some of the great Humble Indie Bundle Games did mess with my sound as I was playing them a lot lately :).