Zim – A Desktop Wiki
It is time to give a shout out to my favorite note taking app: Trilium https://github.com/zadam/triliumPros:  1. Data is saved in SQlite. I am at 33k notes and it springs open instantaneously.    
  2. Notes can be arranged into arbitrarily deep tree. Single note can be placed into multiple places in the tree. (Think soft-links)     
  3. WYSIWYG support (CKEditor)   
  4. Tags, advanced scripting features    
  5. Other ususal wiki stuff like backlinks, note-map etc

Cons:  1. Electron.    
  2. Data is saved in SQlite, not plain text.