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The ability to encrypt filesystems is now built into the Ubuntu installer. Most of the remaining wiki pages presented here are terribly out of date.
ManualFullSystemEncryption may be a better place to start.
Pages
Other encryption systems
TrueCrypt
TrueCrypt - Hidden encrypted volumes using TrueCrypt (GUI)
TruecryptHiddenVolume - Hidden encrypted volumes with TrueCrypt (command line)
ecryptfs