I actually settled on 2 text markdown files. One for short term and one for long term tasks and notes. I usually have a list pending tasks and a list of done tasks in each file somewhere (usually at the top). Sometimes I include some very detailed notes in there too, giving each one it's own h2 title (##) and new sections almost always get added to the top of the file rather than the bottom. I also never delete anything, but I have an '## Archive' section at the bottom where I'll periodically move stuff to. I'll also rearrange the sections sometimes to make them all hang together better.
It gets messy, but it's flexible, and when I run it through a markdown formatter it looks fairly nice.