Just about every configuration feature in OS X is done through "System Preferences" (Preference Panes).
Just about - but not all. There are some audio settings that can only be performed by a very obscure utility ....
Mac OS X 10.4 Help: Using Audio MIDI Setup to configure your audio system
... You can use Audio MIDI Setup to configure the audio input and output devices you use with your computer, such as microphones and audio playback equipment. The settings you can change in Audio MIDI Setup depend on the audio device you are using. For example, you can adjust the level for each channel your audio output device has available, if the device supports changing the level. To learn more about using Audio MIDI Setup, open Audio MIDI Setup, in Applications/Utilities, and choose Help - Audio MIDI Setup Help...Mostly AMS duplicates other preference panes, but the channel bit rates, speaker configuration and output volumes are uniquely managed here. Every few months someone uses AMS to solve some obscure sound related problem, occasionally it's a voodoo cure for other oddities.
It's strange that it persists over so many releases. It should be Pref setting, not a utility. I wonder if it finally goes away in 10.6.
(I have an odd feeling there as a similar utility in MacOS Classic 6 ...)
Java settings are outside System Preferences, too.
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