
I just had a problem because I was rendering an animation and the time counter said "1:30h remaining"! But I cannot lose any time so I found out to run 2 After Effects processes under Leopard. Its pretty easy actually:
cd /Applications/Adobe After Effects CS3/Adobe After Effects CS3.app/Contents/MacOS
./After\ Effects
Be sure to run the app as super user.
Now After Effects starts in the terminal. When it's done the interface appears and everything should work normally.
With this method you are able to run several instances of applications. But it's not always useful. After Effects can use multiprocessing and when you are rendering and working with the other instance there is not much processor power left. But since CS3 Adobe puts a little hidden app into the Adobe After Effects folder with which you can run renderings from the terminal and have full control over the settings.