Hi conrado,
I thought of adding a left panel between the workspaces and the notes. The user should be able to create categories there and organize them hirarchically. The categories are then displayed as a tree and the notes can be "moved" or "linked" to the categories. They act as a kind of filter and the tags (current implementation) then act as a kind of subfilter.
If you think more globally, you can implement categories like tags systemwide to get a hirarchical structure, which is impossible with tags only. Then it will be possible to manage categories for example with an own menuitem and use them more globally. For example you can the "categorize" Files, Dokuments, Contacts, nearly every kind of information...
Thomas