It'd be nice to have the option to open a notebook within the desktop app. This will help someone who's working on multiple projects to quickly jump from project to project without losing their spot. This applies to users who create a notebook for each of their projects and have multiple notes for each project.
PS: For notebooks, I think opening a new tab within the app (like browsers these days) would make it easier to manage. In other words, find individual notes in separate windows, but notebooks in separate tabs within the app.