Hi,

> What are your mental (or other) tools for dealing with this sort
> of complexity?

I don't know about tools for this. But you could use "tagging" ala
GMail to avoid having to use hierarchies of categories. It should
simplify the GUI and the database. I would use an RDBMS instead of an
OODBMS as well.

I'm not sure about the use of YAML for this. Because a "notes table"
in the database could use detailed fields like "title", "message",
"post_date", etc. Maybe use YAML for the message only? :-)

I wouldn't worry about MVC because unless you can share a running
server for the different "Views", the data in an RDBMS is enough to
allow for as many different "Views" as the time brings.

It's interesting, but WikiWikis are awesome as well. Maybe you could
create a "Desktop interface" to the Hiki project:
http://sourceforge.jp/projects/hiki

It uses the "file system" itself. :-) hehe

Cheers,
Joao