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The [|https://code.google.com/p/cryptsetup/ Linux Unified Key System(LUKS)] also for both full and partial disk encryption.
An in-depth tutorial for LUKS setup can be found [https://wiki.archlinux.org/index.php/Dm-crypt/Encrypting_an_entire_system| here] and a simpler one can be found [http://www.hermann-uwe.de/blog/howto-disk-encryption-with-dm-crypt-luks-and-debian| here]
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The tool [http://www.arg0.net/encfs| encfs] runs in the user space and allows the creation of encrypted partitions. These partitions can be mounted once the system has been booted. The tool allows for very strict control over which users can access mounted information once a partition has been decrypted and is suited to applications where a specific user/process accesses the encrypted data.
The encrypted partitions can be defined at variable sizes and the sensitive datastores and applications can be run from within them once the partition has been mounted.
A guide for setting up <tt>encfs</tt> can be found [http://www.howtoforge.com/encrypt-your-data-with-encfs-debian-squeeze-ubuntu-11.10| here].
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