Being able to keep notes on each mockup is great, but currently (tested with Mockups 3.1.5) the text syntax support is a bit patchy.
Some of the syntax works, other syntax works but only anywhere but at the beginning of a line. And some syntax doesn’t work at all – I would especially like to be able to use list syntax.
Checkbox syntax doesn’t work either.
If you were to support links in the Notes pane then entering the edit mode would present a challenge, perhaps it could be reached through a double-click or modifier + click (OS X would be command click). Maybe the possible benefits aren’t worth it, but it might be useful to link to other mockups.
One other thing, it would be nice to see the back of that “Notes” title text at the top of the pane. Once there’s text there, it should be self-explanatory as to what it is and then all it is doing is pushing the content down (on my small Mac display).
Perhaps the “Click here to edit notes. (mouseover text: Click to Edit) could be done away with: