Organizing information

“As We May Think”, Vannevar Bush1945
“UpLib: A Universal Personal Digital Library System”, William C. Janssen and Kris Popat2003
“Designing better file organization around tags, not hierarchies”, Nayuki2017
“Prefer associative ontologies to hierarchical taxonomies”, Andy Matuschak2020
“Spatial Software”, John Palmer2020

“A File Structure for the Complex, the Changing, and the Indeterminate”1965
“Xanalogical Structure, Needed Now More than Ever: Parallel Documents, Deep Links to Content, Deep Versioning, and Deep Re-Use”1999
“A Cosmology for a Different Computer Universe: Data Model, Mechanisms, Virtual Machine and Visualization Infrastructure”2004
“A Graph-Theoretic Introduction to Ted Nelson’s Zzstructures”, Michael J. McGuffin2004

Athens—an open source, local-first Roam Research clone
Foam—an open source Roam Research clone as a Visual Studio Code extension
Roam—“As powerful as a graph database.” SaaS.
Org-roam—“Rudimentary Roam replica with Org-mode”

Nototo

Boorus. Oriented towards media, not text. There are many. Every booru I have seen identifies files by their checksum, usually MD5. It may be better instead to identify them by a perceptual hash.
Hydrus—a cross-platform desktop booru with optional server-based collaboration. Stores tags in a database.
Tabbles—a desktop and Web-based document manager with optional server-based collaboration. Windows-only. Allows chat-like comments on files. Stores tags in a database. Proprietary.
TagSpaces—a cross-platform desktop document manager. Stores tags in filenames or sidecar files.
TMSU—a cross-platform command line tool for tagging files. Can expose a virtual filesystem for accessing files by tag. Stores tags in a database.
AlternativeTo: “Apps tagged with ‘tag-based-file-management’”