I have been running encrypted Ubuntu for two years. I have tried as many methods as I have made installations. I am still waiting for the option in the installer. I have repeated the steps so many times that I simply had to write them in a script. I can’t say it is pretty or finished but it does what it’s supposed to do. It moves a freshly installed Feisty Fawn onto an encrypted partition and encrypts the swap as well. Since it has been more than a week since I wrote the script, I have a thought about making a few fixes.
The script is available here.
Edit 2012-06-28: The link is dead and encryption eventually arrived in Ubuntu alternative installation in a few years time. This post remains as a historical reference.