When comparing CipherShed vs S.S.E. File Encryptor, the Slant community recommends S.S.E. File Encryptor for most people. In the question“What are the best file encryption tools?” S.S.E. File Encryptor is ranked 15th while CipherShed is ranked 18th.
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Pros
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
Pro Cross-platform file-encryption
Pro Choice of strong encryption algorithms
Cons
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.
Con Not intuitive
But it works if you read the instructions.