I’ve been using Ulysses as a note repository for the last 18 months or so, before and after reading the book. Its main weakness is in linking sheets easily but I’ve written a couple of solutions which work great for me. One advantage is you can use whatever title you want for your sheets and links rather than having long date stamps that clutter things up without adding meaning. Links are cross-platform and when hooked up with OmniFocus or Filemaker (Go) make for a pretty seamless experience across devices.