When comparing ecryptfs vs EncFS, the Slant community recommends EncFS for most people. In the question“What are the best file encryption tools?” EncFS is ranked 5th while ecryptfs is ranked 10th. The most important reason people chose EncFS is:
This makes it suitable for using with Dropbox or similar cloud storage platforms.
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Pros
Pro Encrypt your home directory
The entire user home directory or folder inside can be encrypted and unlocked during login.
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.
Cons
Con No single file encryption
Can't request a single file be encrypted.
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.