I stumbled upon encFS (http://www.arg0.net/encfs), which encrypts your data on top of a current filesystem, but it uses the folder structure of the underlying filesystem.
You can use encFS for Dropbox or other cloud storage as it does a one-to-one mapping between files and encrypted files. It has even a setting to let you not encrypt the filenames but only the data contained.
This is great news as you can browse your Dropbox website for removed files and you can restore them, even though they are encrypted.
Installing or building encfs on Mac OS X is a pain, which why I used Homebrew (http://mxcl.github.com/homebrew/) to install it.
Before I started using encFS, I did a few tests and things like rsynced to encFS. I got failures with that. The homebrew version of encFS does change the date/time of the destination when changing the date/time on links, not the link itself.
I looked at the code and it became clear how to fix that. While at it, I’m now using macosx.fuse (http://osxfuse.github.com) as Fuse, which is newer than the fuse version brew is using (fuse4x) .
Compiling encFS is a pain, so I’ve created a script to install it. Have a try at https://github.com/jollyjinx/encfs.macosx .