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When comparing EncFS vs CipherShed, the Slant community recommends EncFS for most people. In the question“What are the best file encryption tools?” EncFS is ranked 5th while CipherShed is ranked 18th. The most important reason people chose EncFS is:
This makes it suitable for using with Dropbox or similar cloud storage platforms.
Question Ranking
Pros
Pro Encrypts on per-file basis
This makes it suitable for using with Dropbox or similar cloud storage platforms.
Pro Cross-platform
Works on Linux, OS X and experimentally on Windows.
Pro Configuration is stored in the working directory
The configuration for EncFS is in the form of a dotfile (.encfs6.xml) and it's stored in the working directory. This way you only have to remember the passphrase because all the other metadata is stored in the configuration file.
Pro Built on top of TrueCrypt
CipherShed is built on top of the famous and now abandoned TrueCrypt and it comes with a lot of things that TrueCrypt had.
Pro Completely free
CipherShed is completely free and open source.
Pro Cross-platform
Available on Windows, OS X and Linux
Cons
Con Not up to speed with modern cryptography practices
From some audits in the past, EncFS has had some issues with being up-to-date as far as cryptography practices go. For example, it uses the same key for encryption and authentication or file holes not being authenticated.
Con Difficult to enhance key derivation
Since CipherShed decided to keep the TrueCrypt compatibility, and stick with that format they also have to stick with TrueCrypt's key derivation which was released in 2004 and understandably does not offer the same security that it did when first released.
