I don't want to sound like a fanboy, but I do just love org-mode. Of course, I was already using Emacs for development, and org-mode just slips seamlessly right in. Everyone seems to suggest some other service where the data is stored in a proprietary format on someone else's server, but I do very much like keeping control of my own data.
Just the tables feature (http://orgmode.org/manual/Tables.html) alone is worth it, but inline LaTeX comes close. Mixing math in LaTeX with a proper table editor (unlike LaTeX) and being able to export to anything that matters (HTML, PDF and LaTeX) -- bliss!
I picked up org-mode again after trying a few online tools (including Google Docs and Trello), only this time spending an entire day reading the docs and a few blog posts on customisation before putting it into use.
The day ended with a "(add-hook 'after-init-hook '(lambda () (org-agenda-list 1)))" at the end of my .emacs file.
It was totally worth it. I am more organised now and as someone who gets distracted easily and may have a slight case of Adult ADHD, it has had a positive effect in my life. Just add Dropbox to the mix and it becomes all the more awesome. As you said, I love it how it just 'fits' in with Emacs when writing code.
Learning org-mode is not a wasted effort. There is just so many things that you can do with it once you know what you want.