GTD on Devonthink: Thematic notes
Thematic notes are also stored under "Reference materials". When a thematic note include referencing, this is usually done in the form of the bibliographical reference also stored in the "Reference materials" folder. Just typing the reference in quest automatically create a wiki link to the bibliographical reference, which can be easily navigated.
Only one folder is used for the whole range of of the notes kept in "Reference materials", which are simply sorted by alphabetical order.
This has replaced what I previously kept in my filemaker database and in Scribe.