After updating or installing new software my audio is muted

Sometimes when you install new software or an update on a digital audio out Mac, the sound output gets reset to 96 kHz, and as a result, certain applications may no longer give you sound out. Instructions for resetting it are on this article:

http://docs.info.apple.com/article.html?artnum=300832

Sometimes if the machine is under 4 years old, the PRAM chip gets reset or the NVRAM chip gets reset, and audio out won't work on any application. Resetting the PRAM normally fixes this issue:

How to Reset NVRAM on your Mac - Apple Support

If your machine has a backup battery (also known as clock battery, or battery part number on non-notebook computers) and is over 4 years old, it may need replacing, as the PRAM will be in a constant state of flux:

Macintosh Family: Batteries and Part Numbers, Part 2 - Apple Support

This can in turn cause audio to fail across the system.

Some third party USB audio devices may fail if their drivers installed are not updated for the operating system in question. Some are sensitive to Energy Saver from closing the lid of a notbook, or running Sleep from the menu of the computer, or automatic Energy Saver settings in Apple menu -> System Preferences -> Energy Saver. Use Screen Saver instead, or ask the third party look at better supporting Apple's Energy Saver with their audio device.

An early release of 10.4.10 for Intel Macs had an issue which has since been resolved with the Audio Update 2007-001.