I usually take notes:

• On a piece of paper if it's about a book I'm reading (I use the paper as a bookmark, and usually finish the book with 2 or 3 sheets of notes)
• In Google Docs if I'm brainstorming stuff at a computer or if it's on web content
• In a notebook if it's from thoughts/discussion with people
• (rarely) directly into Anki on my phone if it's convenient

I then will usually go over those to enter into Anki the bits that are worth remembering (striking them out from my notes if necessary).

I usually use a four-colored pen for notes with the following rule:

• Black is for info about what I'm reading (summary, quotes, interesting bits)
• Blue is for commentary on the above ("I didn't understand this", what if, questions, "this reminds me of...")
• Red is for important stuff
• (Green is for other: highlighting special stuff, off-topic, etc.)

My google docs are sorted in folders, and I usually start them with a bunch of keywords to make them easier to search (I have browser "quick search" keywords, where entering "md whatchamacallit" will return a search in My Docs).

I go into some details here.