I use Notational Velocity (actually nvALT, it's successor) and also have this integrated with 'QuickQuestion' (available as qq in my terminal), and configured so all notes are formatted in plain text in the same folder, and backed up to a simplenote storage service. In addition to the NV and QQ interfaces to my notes, I tend to keep a sublime text project wired up to that same folder. And simplenote means I can get to these from my phone as well. I've tinkered with extending this setup with Anki, for topics that I want or need to learn and integrate more thoroughly (Anki = spaced repetition learning). Beyond these, I've got a mess in Evernote, Pocket, and others. I've been experimenting with voice-recorded (then transcribed) reminders in Google Keep when I'm on the go and cannot type or write my thoughts down. And I still always rely on a good pen and paper notebook to synthesize my day each morning, or the evening before! :)