I've spent a lot of time thinking about TODO lists and trying different solutions. Eventually, I settled on a very specific means of using good, old, pen-and-paper.
I think probably the most important feature of the TODO list is that it gives you mental clarity. Both the popular book "Getting Things Done" and a career couch I worked with for several months talk about the importance of clearing the mind before being able to begin work in earnest. If you have "do the laundry" stuck in your head, it's going to be a major hurdle for getting through work. So, having some sort of system to capture everything that needs to be done is essential for staying on task with work.
So that means that the most important feature of TODO is capture. Any system that imposes overhead on capturing items for your TODO list will eventually fall out of habit. You'll start to mentally prioritize which things go on the list and which things do not. That ultimately defeats the purpose of the TODO list, to get things out of mind, squirreled away in a safe place.
Thus, very formal issue trackers like BugZilla or Redmine (or anything else that has a separate "issue entry page") are far too cumbersome for capture.
But being streamlined on capture is not the whole solution. Having used sites like PivotalTracker or Trello, I've fallen into traps of recording TOO much. Certain pie-in-the-sky tasks will sit in the list for months on end, getting no closer to ever getting worked on. It then becomes its own mental burden, worrying about whether or not certain TODO items will end up in that moribund pile. I even tried writing my own that had an arbitrary limit to the number of items I could enter. It just didn't feel right. It was always too easy to just bump up the limit and keep adding items.
So with all of my experience with various activity and issue tracking systems, I went straight back to pen and paper. My system is very simple, but it is not from lack of design. Its simplicity is the design.
I use an ink pen on a yellow legal pad. The pads are cheap and readily available. The ink requires strike-throughs for error corrections. I write in two columns, but only to be able to use all of the paper. There is no semantic difference between the two columns.
I do not number things, unless I'm in crunch mode and am working very fast through a series of items. I am more likely to underline the high priority items, rather than number them. I don't think it's really possible to prioritize things any more than "things I'm working on in the next few hours" versus "things I'm not working on soon." Anything more than that really calls into question the entire concept of priority for me. It's easy enough to scan the list and figure out priority as I work. I can also rewrite the list with higher priority items at the top if necessary. Usually it's not necessary.
Completed items get scratched out, fairly heavily. The goal is then to fill the page with ink. It becomes a motivating factor to finish the last few items on the list.
The list is limited to 2 columns only and is not allowed to spill on to a second page. I rewrite the list either once a week or (more often) when the page is full to remove the completed items. I did three columns for a while, but it started to develop a deadpool at the bottom right end of the page, so I went back to two columns. Multiple pages would be even worse, and would make it harder to scan the total list. That basically means I'm limited to a max of 50 or so active items on my TODO list. I've found that, if I need much more than 50, then I've failed to manage my work correctly. The desire to record more is a signal that I'm procrastinating things and taking on too many commitments.
And that's it. Any other feature of TODO list tracking is either too restricting on capture or too enabling on over capture. Pen and paper is it for me.