Some new minihowtos about how to run ubuntu linux encrypted is made. When you run ubuntu encrypted, the only difference is, that you have to insert a passphrase every time you boot up your ubuntu, and the speed will be slightly slower (hardly noticeable).
This mean, that you can perfectly well run Freenet from an encrypted ubuntu. When you have finished using the encrypted ubuntu you will have to log out and switch of the computer, and to let it cool of for about 10 minutes, for its contents to be safe. There are also some minihowtos about how to encrypt your files or how to run encrypted directories (encfs). So in reality you can run an encrypted file in an encrypted directory in an encrypted ubuntu linux - as well as run freenet from an encrypted ubuntu (linux). The website is: http://www.minihowto.org :-)