This isn’t really a knowledge base but it’s how I keep my files and information. I have three kinds of data: paper notebooks, loose papers, and computer files.
The notebooks are for things that come into my mind, designing software, notes when learning something, small bits of important information and general writing of various kinds. These live on my bookshelf but they move all around. Each notebook has an ID and a topic for example, “learn/math/topology”, or just “organization” which is where I put important information and lists.
The loose papers are mostly for bills, letters and forms. I have a box with a bunch of plastic wallets and loose papers. I toss letters and stuff in that box and every 2-3 years or so I sort through it and put them in the wallets (which are marked by topic).
For computer files, my home directories on my two computers are sorted by topic using the same scheme as the other two kinds of data storage. Periodically I move them to a HDD containing archives and backups. The archive directory is first sorted by calendar quarter then by topic (since what fits in a topic can change over time). The backups just contain recent snapshots of various drives. The whole thing gets compressed and copied to a server running at my mom’s house.
This works just fine for me because when I want to reference something, I usually know the topic and roughly where it’s stored. It’s hard to find things you read on a website/read in a book/saw in a video/heard in a podcast if you can’t remember enough of the title. I think these cases except for the first aren’t well solved by PKBs at the moment.
I used to use evernote first then dynalist but moved away from both 4 years ago due to how slow they were on my iphone 5s. Instead I just bring a pen and small notebook or piece of paper for thought capture which is as fast as anything could be.