Trilium Notes is a hierarchical note taking application with focus on building large personal knowledge bases.
Ranked in these QuestionsQuestion Ranking
Pro Free and open source software
Pro Excellent WYSIWYG interface
Pro Database storage rather than files
This enables the tool to do a lot of things that would be difficult with plain text file storage.
Pro Note encryption
Pro Note versioning
Pro Synchronization with a server
You can set up synchronization but you need a server to do this.
Pro Graph of node connectivity
Pro Attributes that can be assigned to nodes and inherited
Pro Archival functionality
Con Interface can be confusing
There is a fair amount of flexibility to the interface but it can also become confusing, especially when some parts are not necessarily simple to use. Most of the basic features nevertheless are intuitive.
Con Database storage rather than files
This makes it a little less simple to work with (also has benefits).
Con Not markdown
It will import and export markdown but it does not store content as markdown. This isn't necessarily a problem if you don't need it.
Con Synchronization requires use of Trilium's sync server
This can be problematic to set up unless you have a web server that will support the requirements of this.