I was taught a specific method in HS and never looked back. I've added a bit of my own style but not too much deviance.
I use National's quad, redish brown cover. Numbered pages, cloth spine and heavy duty cover. I won't use anything else.
Each project has it's own book, unless it's small, then it goes into the "misc" book. Where I will detail small (30 pgs max) and with a division of each project clearly marked.
There is always a title page, with name, start date, any collaborator's names. Generally I put the institution as well, and the group I work within. From there, there is a table of contents that I leave a few pages (4, front and back) as room to grow.
Each day's work is done chronologically, with a time of start and end, in addition to the date. There is always 1/2'' I use for footer notes. All foot notes are dated and done in green pen. There is a clear distinction between the foot notes and the original work.
IF I conduct research in a new lab or strange location, I make note of it. It'll be under the day's title/date. I like to keep track of when I'm in a different location just in case something wonky happens that day.
I use a black pen for all my calculations and only single-line scratch out incorrect work or words. Green pen for foot notes, and red pen for special occasions where an adviser noted something. This is rare, as I'm a stickler for accuracy. If it's not critical, I'll put a sticky note in, written in red pen.
If a collaborator has to use my book for any sort of sample prep, they are to follow my format, and indicate that they were doing the work. I also require them to sign their name at the end of the entry. I've only had to do this once, and it makes me feel icky. Even though they were only putting in some dilution calculations and making some samples for me. It seems weird regardless. I want it to be clearly indicated that they were in my book.
I also have 10 pages front and back at the end of the notebook saved for references. If I source work during my research, I will put the citation there, by hand. It's nice to have there. If I reference it within the lab book, I will indicate so in the footnotes. This includes equations and methods from textbooks. Even if it isn't going to go into the paper to be written, it's nice for me to personally have. I have a crazy brain, and I like the reminder. "Oh ---? Where did I get this from?" With a note of the text it was from, I can easily remind myself.
Edit: The book stays in the lab. If I need additional copies of information, I take a photo copy, and indicate in the footnote that a photo copy was made of said page, at what time, and for what purpose. All additional photo copies are returned to the lab book or destroyed. It depends on what I'm working on.
It needs to be explicitly clear what I was doing, step by step. And as neatly as possible.
