Personal Knowledge Management zim a desktop wiki feather wiki is a light weight tiddlywiki
Fernando Borretti discussed issues with note taking tools1, particularly self-built tools that attempt to universal solve note taking. He concludes that purpose specific apps are the best (e.g. have a journaling app, a TODO app, etc.).
apple-notes-liberator is an extractor for Apple Notes to convert to JSON
Zotero is a useful cross-platform reference manager and windingwind/zotero-better-notes note taking within zotero that offers Roam like features within Zotero