Zim – A Desktop Wiki
It is time to give a shout out to my favorite note taking app: Trilium <a href="https://github.com/zadam/trilium" rel="nofollow">https://github.com/zadam/trilium</a><p>Pros:<p><pre><code>  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
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Cons:<p><pre><code>  1. Electron.    
  2. Data is saved in SQlite, not plain text.</code></pre>