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I don't use it for whole ~/ encryption (though there's PAM modules to automagically mount it on user login if that's what you're looking for) but just directories. It's lightweight process-wise, doesn't have exotic dependencies, is distro-agnostic (just copy the directory tree over and encfs-mount it somewhere), by default root hasn't access to mounted EncFS file systems, it doesn't seem to corrupt easily when not properly umounted beforehand like with spontaneous reboots (though obviously open file handles will always be problematic no matter what you use), is easy to use and make backups of. Plus you probably could mount an EncFS inside an EncFS.
Any more specific questions?
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