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In addition to local Time Machine backups, I would like to automatically backup my working data from my Macbook to a remote FTP space. Because it's a location I don't control and sensitive data, I want to use encryption.

There are some approaches floating around the 'net how to achieve this, for example this tutorial that uses duplicity and works great (I've tested it).

However, all these approaches generate file archives of some sort (tars in the latter example). I would like to have a backup where I can access every file individually, but encrypted. So the backup structure would look something like this: 

 Work
  Documents
     Letter to Mr.T.doc.encrypted
     Expenses.txt.encrypted
  Images
     Sunshine.jpg.encrypted

does anybody know a tool that can achieve this?

Alternatively, is there a stand-alone OS X command that can encrypt files? I might be able to use that in combination with rsync to build this on my own.

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    These don't directly solve the issue as you'd like, but here are the methods I've used: #1 - Create an encrypted disc image. Mount it and drop the files you'd like to backup into it. Have some utility to sync this remotely (I use SugarSync). #2 - Use CrashPlan [free year membership here] (crashplan.com/carboniteswitcher) to backup to their encrypted cloud. In CrashPlan settings you can create a custom 448-bit encryption key to encrypt the backup.
    – bispymusic
    Commented Mar 2, 2013 at 19:01

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This question is a subset of: Tools to compress and encrypt files

See answer here: https://apple.stackexchange.com/a/32732/43002 for built-in command line utilities which (with some scripting) will do what you want. (Such as zip -P and open-ssl)

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