I use Obsidian. Stores everything in markdown and has a nice sql-query-like plugin, dataview, that I’ve built a nice workflow around. Obsidian isn’t FOSS, which has become more important for me, so I’m looking to migrate over to markdown oxide in helix. If I were starting from scratch I might try logseq or similar. Whatever you choose, I think it’s helpful that it’s stored in a portable format like md so you can change programs if you need.