How can I clean up old notes left in my Gmail account by notes.app?
It appears that the following search will find all messages created by Notes.app, and, for me at least, no messages not created by it:

from:username@gmail.com -in:drafts -in:sent -in:chats -l:SMS


(Where username is my Gmail username.  The SMS label is used by the SMS Backup+ android app, which stores SMS messages in Gmail in a similar way to Notes.app, albeit under a different label.)

To find messages which are no longer "live" in Notes.app (i.e., are older versions or deleted notes), and also exclude any other labels like SMS, use "-has:userlabels", like this:

from:username@gmail.com -in:drafts -in:sent -in:chats -has:userlabels 


N.B.: For me the results are 100% old or deleted Notes.app notes, but this search will find any other messages created in the same way (i.e., via the IMAP interface, with your address in the from field) so have a look through the search results carefully before doing any mass deletions, just to be on the safe side!