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Howtoforge posted a tutorial about encrypting directories/partitions with eCryptfs on Debian Squeeze

eCryptfs is a POSIX-compliant enterprise-class stacked cryptographic filesystem for Linux. You can use it to encrypt partitions and also directories that don't use a partition of their own, no matter the underlying filesystem, partition type, etc. This tutorial shows how to use eCryptfs to encrypt a directory on Debian Squeeze.
  How To Encrypt Directories/Partitions With eCryptfs On Debian Squeeze