How do I configure apt to use a Proxy.pac file?

In system --> preferences --> network proxy, enable Automatic proxy configuration and enter the URL of the PAC.

Then press apply system wide, and that should do the trick.

sudo apt-get update failed (on a fresh 11.04 VM) after following the instructions in DemonWareXT's answer (System -> Preferences -> Network Proxy).

I followed the instructions I found in help.ubuntu.com/community/AptGet (under "APT configuration file method") and then it worked.