The tool matters less than the habit, but the right tool can make the habit easier. Here are the ones I keep recommending.
Obsidian
The default for most people. Local markdown files, excellent linking, a healthy plugin ecosystem, and a web clipper that produces clean prose. Most posts here assume you're using Obsidian or something Obsidian-shaped.
Save
A browser extension that turns any web page into clean markdown, with a small local app to organize what you save. Lighter than Obsidian, ideal if your minibases are mostly web clippings. Full disclosure: I built it.
Logseq, Reor, plain folders
Logseq for outliner-brained people. Reor for those who want semantic search out of the box. Plain folders of markdown for the stubborn minimalists. All of them work.
Public minibases worth studying
Some of the best examples of minibases out there aren't called minibases. Andrej Karpathy's reading list, Gwern's site, well-curated Are.na channels. Case studies in what good curation looks like.