I recently read "Pragmatic Thinking and Learning", and the author recommends setting up a personal wiki for stuff like this (and for personal notes in general). A wiki is a good fit for an idea repository because it's easy to link ideas together, have them reference each other, etc. I installed Zim Wiki a few days ago and am already feeling like my mind is less fragmented.
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.
I concur -- org mode is fantastic. I've only started using it recently, but I think it'd be safe to say that I'll use it forever.
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 used org-mode before but I didn't put enough effort in learning it. Plain .txt files worked but I started missing linking between 'Notes' or 'Tasks' after a while.
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.
YMMV; I've used Zim for a few years, and I find it useful to track things to do and some work-related stuff; however I don't feel it comparable to the "spark file". I must try this one.
I was trying to find something that would work on Ubuntu and Windows, and where I could keep data in Dropbox. Zim does the former and mostly does the latter; I didn't find anything else that did both.
