>>>> Back in the old days there was ScriptBase, but that only had a hundred
drawers (or something like that).

Everything ScriptBase could do is now available in OS X through the often
ignored Database Events. I'm not sure how helpful it would be for organizing
and storing scripts, though.

> How can I use SD to organize my scripts?

The one place in Script Debugger (that I know of) where you can store and
edit scripts is in the Clipping window (Windows menu> Inspectors>Clippings)

You can create nested submenus by adding folders to the directory in the
Finder. That's well suited to storing snippets that will be used as part of
a script.

You can also do the same thing using the scripts menu in the menu bar, but
that's more suited to storing scripts you want to execute from the menu bar.

I'm not sure if there is a good, well thought way to organize and store
AppleScripts.
(I just use the finder and dump mine in huge folders).

HTH,

ES