This is a brain dump on how I get things done. I have read Getting things done, Pragmatic thinking and learning and consumed lots of other people's thoughts on such matters. My way of doing things is what has currently emerged from my brain as habits after processing all that.
It seems to do me well to write thoughts down as I have them. I do that as much as I can. If it is in electronic form, it goes straight into text files which I keep in Dropbox. If it is on paper well, it stays on that paper. But if it feels relevant and I do not act on it pretty soon I will transfer it to text files and throw the paper away.
I usually keep a text file open while I work, writing things into it a lot more than I read. Unless it is focused on a very clear subject I will simply name it with the creation date.
For things which feel clearly actionable and which I am not about to do right away, I keep a few todo lists. My current app of choice for this is Clear. I keep as few lists as possible, and I try to be aggressive about checking or deleting tasks. I have noticed very clearly how bad items sitting around on todo lists are, so if some task has been sitting around for a while I put it in a text file. Clear should contain clear action items which I have already decided how do go about, and - most often for work - pointers on where to pick up next time the context appears. So I put fuzzy stuff in there "Investigate X" sometimes as a reminder of something to start on when I get to work. If a few days pass without me getting to it, I will delete it (probably putting a line or two about the subject in a text file).
Most larger things I work on will have their own text file, and they often contain lists of things to do. Fuzzy tasks like above often have thoughts or a bunch of clear things to do in the project's ever growing text file.
I guess you could say that the to do lists in Clear are the next steps for things which I am not focusing on at the moment. Yes, that sounds about right. Text files are both for the thing I am doing right now and for long-term storage.
Out and about, Clear naturally gets more use for tasks and text files stand back until I get a chance to sit down and write.
This seems to be a good balance between structure and flexibility for me. When I get lists or tasks from other people, I often transfer relevant parts to a text file and work on it there in my own words.
Related to all this, I have noticed a danger for any kind of list to start feeling like one to do and work through. For that reason, I keep from making "maybe"-type lists, or lists of films to watch, in Clear and put thoughts like that straight into text files instead. But hey, life can be tough when even the stack of unread books next to the bed start shooting you demanding glances after a while.