I think in this case, "home" encryption is what I use. Most Linux systems when you install will offer to encrypt your home folder. When you login, your password unlocks a key which ecryptfs uses to virtually mount a directory filled with encrypted files to be your home directory. As long as you are logged in, the home directory contents are available (transparently). When you logout, the virtual mount is destroyed, leaving behind only the encrypted files.

To put it in perspective, if you were logged out completely and tried to login remotely, you would be forced to use a password login initially. If it was more like my desktop where I'm logged in and the screen in locked, the home folder is unlocked, so I can remotely ssh in using just my keys.