When comparing BitLocker 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 BitLocker is ranked 12th. 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 Native Windows support
It offers the best integration, ease of use and support with Ultimate and Enterprise editions of Microsoft's Windows Vista and Windows 7, and with the Pro and Enterprise editions of Windows 8.
Pro Volume-based encryption
BitLocker allows encrypting an entire volume including the OS.
Pro Multiple authentication methods
You can use a combination of methods consisting of Trusted Platform Module, PIN, and a passphrase on a USB thumb stick.
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 Proprietary
No public audits possible.
Microsoft could want or be legally required to puts backdoors without users knowledge.
Con Not available on Windows home versions
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.