I'm in a very similar boat. My best solution so far has been to use Onenote and Outlook plus paper, but I'm looking for something better. Maybe org-mode or a personal wiki?
In Outlook I mark emails that I want to respond to/deal with later as "unread" or else apply the "followup" flag depending on how much work responding will take. There are downsides but I have so far been able to keep the scheme manageable (single-digit quantities with the unread/followup tags at any given time).
I use a paper notebook, physical sticky notes, and scraps of paper for general notes depending on how ephemeral their importance is.
I use Onenote for meeting notes and a running to-do list, as well as a rough knowledge base, but it's far from perfect:
- You can organize notes but you are sort of locked into the organization scheme that you start with. If you discover some orthogonal knowledge organization/symmetry across topics, there's not a good way to reorganize. For instance, say a certain topic gets discussed in different contexts in different weekly meetings. If you already have note sections with deep histories for Meeting 1 and for Meeting 2, how do you link instances of Topic A across meetings in some useful way?
- For to-do lists, it's easy to start with one list of all your tasks, but as these get complicated with subtasks, you might organize them into different sections, and eventually different pages... but now the to-do list is actually spread across fifteen different note sections, and are you really going to read each one at the start of each day?
It strikes me that the central problem is that the tree structure is not the right one for notes. A wiki might be better. However, the portability and convenience of Onenote despite the shortcomings (for my needs) make me hesitant to try anything else.