Cherrytree, no question. You can make hierarchical lists/notes, hyperlink to files, folders, websites and other nodes (lists). You can also insert tables and images in your entries and format text. The whole thing is saved as a single file and you can choose for it to be encrypted if you want. I sync it between devices using Syncthing. Both are FOSS, private and secure. Cherrytree's UI doesn't look especially modern but is very effective and you can make your own themes for it in the preferences if you want to glam it up a bit. You can pretty much use it as a wiki for your entire life. In fact, if I could only have one application on my computer it would be this!