Every Monday, I dump into the weekly TODO list every task which has to happen that week, plus whatever I think is reasonable to do otherwise.
From the weekly TODO list, every day I take some topics to the "today" list. All the things with a strict deadline have a calendar entry associated with them.
If anything pops up during the day, it goes to the daily or weekly TODO list.
On Fridays I see how much of the list I managed to do, how many items came in, where they went. The remainder of the weekly list goes into the relevant topics list.
If I have a lot of stuff left over from the Monday's dump, I try to figure out why it happened and what I can do to plan better next time.
This way I don't have long-term topics mixed with short-term ones, which I found is of great help. I avoid pulling tasks from the topic lists into weekly list if there is something else that needs doing and is not blocked.
This has worked for me reasonably well, I use the same system outside of work.
In org mode I keep one big log.org file with sections split by month, projects get their own sections.
I used to use Evernote and todoist and trello.
For work - paper. Cross an item out when it’s done.