I'll split it into three parts. First, you want to know what the book is about and whether it's worth reading. Second, your notes should summarize the core of it, so that as soon as you glance your notes, you understand what it's about. Third, and optionally, you want to criticize the book and compare it to similar books on the topic.
Before reading: Outline the book
Find out what kind of book it is - scientific, practical, philosophical, or historical. Some books, like Flow, are usually read by people for practical reasons, but it's philosophical in writing. The difference between scientific and philosophical is that philosophy expects no prerequisite knowledge, whereas scientific is unreadable without knowledge.
If it's a practical book, your notes should be focused around what to do. If it hasn't clearly explained what to do, then it's useless.
Get an overview of the book. Reading reviews or online summaries helps. Intro is great. Simplify it into one line what it really teaches you.
Skim the table of contents. Most books summarize a chapter at the end of each chapter or beginning. Get a feel of the skeleton of the book.
By now, you've skimmed the whole book, congratulations.
If it's a good book, it will tempt you read it in detail. If it's not, don't waste any more time on it. There are lots of books worth reading.
While reading: Terms and propositions
Put aside a section of your notes as a glossary of terms. This is extra useful for scientific books, where a term is often repeated, and philosophy, where different books use the same term to mean different things. Business books can be especially frustrating without defining terms.
Every time you see a new term, write it down in the glossary. You'll know a term is important when several paragraphs and figures are written to define it. The term might act as a pillar, supporting a whole chapter at times.
Next, write down propositions. What is the book trying to explain? A good book will be extremely dense - several propositions in just a few paragraphs. Some bad self-help books might only have one per chapter. The harder books will usually be most information dense and hardest to read, and this identifies them. Read them slowly.
After reading: What's the point of the book?
If you have properly read the book, it should elevate your knowledge to the same level as the author. Now you should criticize the book. If you have nothing to criticize, it either said little, or your understanding is not good enough.
Is the book true?
Check if the book is understood properly and dispute is not contentious. If criticizing, show where the author is uninformed, misinformed, or illogical. Otherwise what she says is not false, but incomplete.
What now? How does this change you? What do you do? If the book is practical, it must be acted upon. Otherwise, it is incorrect. Ask yourself why you don't act upon it.
This last part is actually quite exhausting to do and I recommend you skip it if you're still new or if the book just wasn't that good.