When trying to synchronise your Tomboy notes using SSHfs to a location you know already contains your notes, you may get this error:

fuse: mountpoint is not empty
fuse: if you are sure this is safe, use the 'nonempty' mount option

From what I understand, Tomboy expects an empty directory to start synchronising notes, and if your directory is non-empty (for instances, you've reinstalled your system and are setting up your Tomboy instance to start syncing from that directory again), Tomboy will complain and refuse to sync.
It will, however give you the solution (“use the 'nonempty' mount option“) but not tell you how to do so.

It turns out you can add options to the “Folder Path (optional):” box, just do as if you were on the command line: -o option whatever, or in this case -o nonempty
You can also specify a port on which to connect using SSH, if you're using a non-standard port.

So, for me, the three fields in the Tomboy sync look like this:

Server: thisisabore.net:1337
Username: thisisabore
Folder Path (optional): /home/thisisabore/sync/notes/ -o nonempty

And there, Tomboy will now download your notes, and prompt you everytime there's a conflict between the local and distant notes.

Now, I just have to go through all the differences between these… oh, what fun.