The primary two methods that I use to capture information is by taking notes and by clipping and storing web pages and PDFs.
Today I mostly use Tiddlywiki, OneNote, and Standard Notes to take notes and Evernote for clipping and storing information. My use of these applications has evolved over time. I've been using Evernote the longest and then moved on to OneNote, Standard Notes, and Tiddlywiki. I continue to use each one of these apps for different use cases.
Welcome to the Note Taking Apocalypse promotes wiki-style links in notetaking apps.
Twelve Best Note Taking Apps page
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Places To Put Stuff