Where does OS X Mountain Lion store Notes data?
Notes are stored as HTML in an apparently non-standard binary format in ~/Library/Containers/com.apple.Notes/Data/Library/Notes/NotesV1.storedata-wal.
You can grep for known note contents on the command line, or print all notes (stored as HTML):
cat ~/Library/Containers/com.apple.Notes/Data/Library/Notes/NotesV1.storedata-wal | grep -aio '<html>.*</html>'
While I was writing this answer, I also had the problem once that Notes restarted with data reset. The next launch, everything was there again, even though I had created new notes after the reset (so both the old and new notes existed on third launch). Maybe just try quitting and starting Notes again?
I found this article which appears to help: http://applehelpwriter.com/2013/03/02/how-to-recover-disappearing-notes/
cd ~/Library/Containers/com.apple.Notes/Data/Library/Notes; strings NotesV1.storedata | grep body | open -f
On OS X Lion (10.7), I found my notes in the file below.
~/Library/StickiesDatabase