Rated 4 out of 5 stars
1) Can I see all-notes list - for example, if I forget to what message note attached?
2) Can I make note to folder?
ad 1) Notes are stored in the "XNote" directory under the Thunderbird profile directory (http://kb.mozillazine.org/Profile_folder_-_Thunderbird) - unless you changed it. You can open the files with any text editor.
ad 2) No, because notes are tied to a mail's message identifier.