(This is especially relevant for things like task lists, plans etc., where things often change substantially over time, though it's important not to overdo it and "lose" context etc.)
TODO lists in particular, I feel gets stale very quickly and accumulates obsolete info.
I now write clearly visible headings and maintain chronological order. I often color code the headings: just underlining or highlighting the title with subject color makes it easy to find. Thid, with chronological order ingeneral, works well for me in lieu of a table of contents. YMMV.
I find that this works for me. I keep the journal in hand-writing form, and subject files digital. This also has the advantage from my perspective of keeping my thought process on an analog medium that is easier to control.
I also keep a paper notebook for software engineering, but I find it less convenient than my old chemistry lab notebooks were. The problem is that in my software engineering job, I must alternate between tasks and meetings many times a day. So either I keep things strictly chronological and have a difficult time maintaining a usable table of contents, or I have a new page for each of the day's projects, at the cost of constantly jumping from page to page and inefficient use of the notebook's space. I've yet to find a happy solution.