MySQL - The world's most popular open source database
Freeplane - Freeplane is a powerful and free software for building mind maps.
PostgreSQL - PostgreSQL is a powerful, open source object-relational database system.
Linked Ideas - A macOS/iOS apps to treat ideas as links of concepts.
SQLite - SQLite Home Page
OmniOutliner - OmniOutliner is a writing app for collecting information, outlining ideas, adding structure to any sort of writing.