How can I change the font used in Preview PDF notes?

Sadly, it is not possible to change the font used by Preview for Notes - this is denoted by Apple an 'UnEditable'.

This thread on the Apple forums (which I can't take credit for) provides a couple of work arounds such as using Annotations instead of notes (as these are editable) or post-editing comments in Adobe Acrobat Reader XI, but not an actual solution to this problem.

Go to Font Book, select Noteworthy, right click and show the font file in Finder. Alternatively you can directly navigate to /System/Library/Fonts

Replace the extension of the Noteworthy font file with .disabled (or .bak, or anything else non-font related). Make sure with the Inspector that the extension has not been re-added by the Finder. This is how it should look:

Re-start Preview, all PDF notes are now shown in Helvetica.

Tested on 10.8 and 10.9.