I created this system which I've mentioned before (AGPL):
http://onemodel.org
...because it tracks all my thoughts, plans, & resulting to-dos, and I mark them off when done ("archived") in a few keystrokes. Then there is a simple feature for displaying the ~"journal" for a date range which defaults to starting yesterday at midnight: everything created or archived in that time is shown, so I've basically stopped keeping track in any other way, of what I have done, as I can always look it up.
I used to use org-mode, "inspiration" (an old windows program for collapsible outlines and mind maps), and various text editors, but this is the most efficient and flexible I have found. In my use, it is like a textual, ever-expanding comprehensive mind map that is highly efficient to use from the keyboard, uses postgresql, and can handle large amounts of data, having the same thing linked in more than one place, etc etc, so you can organize all possible stuff in arbitrary ways to suit yourself: I tend to use a few hierarchies and some frequent categories go in multiple places, for convenience. I use it to keep lists of gift ideas, calendar, personal journal, and it just gets the job done with the lowest impedance of anything i have tried or heard of. It has an auto "journal-generation" feature, some finicky import/export features to html or to/from text, searching, somewhat limited file storage, and more.
It has no mouse or mobile support yet, but it is the best thing I've found for any kind of note-taking (I'm the author). It needs simpler installation and added features but is stable and works really well, really efficient once you get familiar, and everything is on the screen. I hope to add anki-like features in the future. Contributions welcome. I'm told it needs an introductory screencast, which I plan to put up eventually, but for now there is a tutorial at the web site, on which feedback is welcome.
The latest code is in github, where I am working (very slowly) on an infrastructure for linking or exchanging info between instances.