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There should also be a command "Delete empty notes", which would scan the database for empty notes and ask a confirmation to delete N (count of them) notes.
It should auto-load (optionally?) last used notebook file. You can check azzCardfile program as an example of multi-file handling logic.

Also, it should somehow be compatible with upcoming tabs, which, as you said, would be sections of ONE notebook file. There are several ways how "multi-db-support" and "tabs/sections of db" features could make friends.

The question here if we do allow working with many db's simultaneously.

If the answer is no, things are simple: the program loads one db file and opens all of it's tabs with their names. When the user wants to switch the db, he picks "File > Recent notebooks > (name here)", program closes current tabs, loads another db and opens it's tabs.

If yes, multiple tabs from multiple files should be handled in some way. Variants:
1. Open all tabs from all files in one row.
    1.1. Tab title has only the name of the tab. However, it's containing notebook file may be shown as a hover tooltip for the tab button.
    1.2. Tab titles somehow name the file containing the tab. Like "<FILE>/<TAB_NAME>" or "<FILE>.<TAB_NAME>".
2. Make two rows of tabs, first for files, second for tabs. Not the best though.
3. Make a droplist for selecting one of currently connected db's. If you used foobar2000, it's customizable UI allows both approaches: selecting playlist by clicking tabs, or by picking droplist items.

Just providing ideas. Anyway, the behavior must be well defined before any implementation.
Do you mean tagging tags? :)
Sounds interesting, I think some UI sketches could help understanding the idea.
Is it about assigning specific color to a tag and painting note frame with it?

If no, a) what is "category"? b) "Assigning colors to tags" proposal should be posted.
If you ever do it, please make it optional. With something like "plain text mode". Tried azzCardfile? There's a huge 3 row toolbar by default (formatting, paragraph, etc). Simplicity of CintaNotes is one of the reasons I picked it (and I tried a LOT of apps).

Also, that program has an option to remove all formatting from all notes.
It should be optional.