Pulseaudio comes with a command line interface to control many settings.
We can either load the command line parser
pacmd or we call commands directly in a terminal or script:
pacmd set-sink-volume <index> <volume>
pacmd set-source-volume <index> <volume>
controls the volume of a given sink where
<index> is the sink index (listed with
pacmd list-sinks) and
<volume> is any value from 0 (= Mute) to 65536 = 100%. The configurations files in
~/.pulse are not meant to be read or edited.
In order to control output volume for a given application you may be interested in earcandy . This application is under active development, therfore not yet all features are available in 11.04.
See also notes for this answer.