Seconding Obsidian. I started using it recently (admittedly for TTRPG notes) and I really like it! I haven't done a lot of cross-linking but it seems to work re

Seconding Obsidian. I started using it recently (admittedly for TTRPG notes) and I really like it! I haven't done a lot of cross-linking but it seems to work really well! Even better, it stores everything in plain Markdown files in a folder hierarchy, so you can easily back everything up and/or interact with them outside the app if need be. Even EVEN better, they have mobile apps that are perfectly happy to let you use your own file-syncing mechanism if you want to (although they do offer a sync service of their own as well.) Once I got it set up, everything Just Worked.