When comparing B1 Free Archiver vs EncFS, the Slant community recommends EncFS for most people. In the question“What are the best file encryption tools for Linux?” EncFS is ranked 4th while B1 Free Archiver is ranked 5th. 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 Webapp unarchiver available on their website
A great and unique utility for someone who is on a locked down public workstation, or on someone else's computer, one can unarchive using the B1 Online Archiver here.
Pro Multiplatform
Pro Free
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 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.