For example, running defaults write com.apple.iChat AutoAwayMessage "I went away" will set your auto-away message to "I went away." You may need to restart iChat to force the defaults to reload.
The auto-away timeout is also customizable. Although it defaults to 45 minutes, you can set it to any value greater than iChat's default idle timeout, which is 600 seconds. Running the command defaults write com.apple.iChat AutoAwayDelay 600 will set the auto-away timeout to 600 seconds, or ten minutes.
You can also completely enable or disable auto-away with the AutoAway default (defaults write com.apple.iChat AutoAway -bool NO to disable, or YES to enable).
Note: I have been using some of these settings in Chax (I'm the developer) for some time, but I haven't seen anyone mention them anywhere else.

