When comparing EncFS vs jZip, the Slant community recommends jZip for most people. In the question“What are the best file encryption tools?” jZip is ranked 4th while EncFS is ranked 5th.
Specs
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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 Totally free
Pro Sleek interface
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 Default installation options include adware
You can avoid this if you select your options carefully at installation time