I'm, like you, very interested by this discussion.
Here are what I've been trying/doing
- Onenote : the big vantage point is that it provides you with 2 hyperlinks : one for the desktop app (just prefix it wirh "file:"), and an url for the web app (and therefore, the link works even on android).
By the way, I don't understand that Evernote links doesn't open both in desktop and android platform. Yes, I now the "share link" that works on both platform bur as read only over the web.
- Evernote : works fine. My only concern is that Evernote became more of a family tool, and I can't organize it the way I want.
- Using a special folder within MLO. I wanted to use this, but finaly has not proved successful for me.
Now, there is one tool I'd really love to be fully integrated : Mindmanager (now Mindjet Desktop). I t has everything I could ask to Onenote, plus the Mindmapping presentation I really like to work with (actually its the main purpose of this software), and the "power markers" that are, unlinke onenote, dynamics and can be differents from a document to another. I mean, in Onenote, if you set a marker to be, say "project to prepare", you will have it in all your onenote documents. If you rename it, it remains marked in you document, but the dynamic reference has disappeared. I mean, the icon stays assigned to the text with the old name, if you click on it in the marker menu, instead or deleting it, it adds the same incon with the new name.
In short : I'd like MLO to allow the Mindjet hyperlink to works. It doesn't because the link contains spaces. In the Windows explorer, thay works perfectly.