My note and log process is pretty manual, but I've been tinkering with a system in Evernote for the last 5 years and it has started to really pay off over time. My goal is having a clear log of what I did, when I did it, and any useful references all integrated into my general note-taking system, so perhaps some of these observations could be useful:

1. It is a highly personal process. I've tried copying high-level systems (like GTD and its derivatives), specific note-taking / TODO paradigms, productivity/habit tracking apps, and other journaling approaches, and I've always found that if the system is not built around your own habits and preferences, you will eventually lose motivation. Figuring out your own style seems to be important. Another general principle I’ve found is keeping the tools simple. Mostly text-based, always available offline, built to last, etc. Develop the habits, then adopt fancier tools.

2. For quick context-capturing and bookmarking, I rely on email and Pocket. I prefer email because it is reliable, it'll be here in 20 years, and it is fast to flag a message as "needs attention" or e-mail yourself an important thought or reminder. Pocket seems to just work across all my devices, so I haven't had any reason to branch out. Whenever I have time during the day, I organize this “unorganized” view by either taking care of the item (if it’s a quick article in Pocket or errand in email), skipping it (it’s fine to de-prioritize things until later), or by triaging it into Evernote:

3. I use Evernote for a lot of things (including all my technical notes, paper highlights, personal journaling, my "principles" document, philosophy on nutrition, habit aspirations, workout plans, and so on), but of interest for this question is probably a topic-specific log and backlog system. Near the top of my Evernote shortcuts are four log links (Daily Log, Technical Log, Health Log, Workout Log).

4. Daily Log is where I can make a plan for each day, or put nothing here, or just have a place to ramble (writing down thoughts helps internalize them, after all). This is something of an unstructured personal journal.

5. Technical Log is for all technical work that I undertake (coding train-of-thought, reading papers, reading blog-posts, etc.). In reality, under each date, this log contains a bunch of Evernote links to more detailed notes on specific technical topics, but the big benefit here is being able to look back over the course of a week or month about what kind of insights or interesting concepts I’ve come across. It’s particularly useful to read the day after and get most of the context back quickly. I usually always have this log file opened.

6. Health and workout logs track both metrics and how I generally felt that day (health-wise and workout-wise, respectively). It’s ok to have empty days. The important part is filling in on days when things are particularly bad, or particularly good, so you can reflect.

7. After this, I have a bunch of backlog shortcuts — so when I triage items from Pocket or my email, they go into the appropriate backlog list. Examples for me: Backlog of {ML reading, CS reading, Bio reading, Travel destinations, Video/TV/Movies, Restaurants, Games, Running routes, Books, etc.}. Backlogs are great -- they are lightweight, they can grow indefinitely, and you'll naturally prune them of things that you don't care about after some time. Really, lists are a great way of writing things down! When I'm at a coffee shop, I'll pick and item from one of my reading backlogs, if I'm not already working on something. When I have time to plan a weekend, I can scroll through my recreational backlogs and combine some items to fill out my schedule.

8. I like having a high level view of what I did and what I have coming up on long time scales, and for this I use a big spreadsheet, one sheet per year, one row per week, where all past and future social events, travels, and “macro” events. It’s useful to be able to look back at months or years of events and figure out who you spent time with, how often you traveled, or went out, etc. I prefer the spreadsheet to a calendar app because I don’t feel the pressure of adding specific times and I can keep it uncluttered.

Having a centralized place (along with a calendar or some kind of macro-overview) seems to work well for me, because I can easily cross-reference just about any day of the year to figure out what I did that day, my state of mind that day, and so on.