In no particular order:

+ list/checkbox style todo
+ add hooks for easier scripting (e.g., notes that can be hidden, etc) - maybe
  a developer mode?
+ when holding down a key, display some hint about different mouse actions
  (e.g., when holding alt, change to a resize icon) change tooltip too
+ link notes together (lines like javascript analog clocks)
+ send to back hotkey (what key?)
+ arrows to move (snap to edges (like evilwm))?
+ quick align (like expose, must have undo)
+ snap to edge
+ per note-sync
+ double click on background makes a new note
+ help system
+ if note is being clipped, some cue to the user that this is the case
+ keyboard (create/delete)
+ drawing/sketching (via canvas)
+ mini-map (like photoshop thumbnail)
+ history playback (slider)
+ print stylesheet
+ move event handlers to document rather than per element
? should anything happen if a note is off screen
? undo/redo should save zOrders (may be a bit memory intense to save an
  ordering array)