So I have a few disconnected things to contribute, and this reply has been sitting open on my computer for the best part of a day...

I still haven't figured out a better way than my pen & paper journal that I now keep. I've tried every app out there, but it seems like the best way is still the pen and paper for what I want to accomplish.

It sure has its advantages - for instance, I spent 9am-10am yesterday working on ways to refine my current journalling software, rather than doing actual work. I can't really get quite that sidetracked with pen+paper (or at least, I can't do it as much - I'm sure I could still waste time optimising the correct note-taking procedure &c).

My life revolves around work - therefore what I take notes on is to do lists. My personal life is now a list as well. Namely to do lists for work, personal life (groceries,etc), freelance projects, job #2, personal worky stuff (updates to my website, etc), hubski.

I'm assuming you've seen this then? It's basically lists + some additional bit and bobs to keep things on track. While it was originally made for the 2000s-era manger, a decent amount of it is applicable to modern knowledge work, which is handy. The above-linked bullet journal also deals with a lot of the whole "I need to do these four things today" while also allowing for more stuff to come along and even giving you some room for daylogging.

Journalling

I think there's a definite divide between "actionable" stuff (project notes, lists of next actions, shopping lists) and "reference/archive" (thoughts and reactions, mementos, etc.). And while you can combine the two, I can't help but think that decent archive material is going to get lost amongst the monotony of everyday short-term notes, and things you need to do are going to lose their urgency jammed in between recollections and stuff.

Whenever I have these lists on the computer I end up deleting them to clean up (therefore no recall) or the note taking process when I'm in a meeting or having a quick conversation never makes it to the computer. I personally find it rude and annoying when people are staring at their phones and typing furiously during meetings or desk conversations.

I've tried note-taking on my iPad, but I've found the same - I can make quicker, more natural notes (still) on paper, plus I feel less like I'm blocking people out. If it's an important meeting I generally make sure I transcribe my notes onto the computer (often a Dropbox folder shared with the other people on the project). Actionable items end up on the task list, so I'm not paging through minutes trying to work out what to do later on.

When faced with a problem in my list-making/task-doing regime, I tend to go "I know, I'll make a regularly-running shell script to take care of that!". Then, in Larry Walls, I have two problems, not one.