Some things I'd recommend:
- Keep it chronological, don't try to keep a half dozen notebooks for different subjects or projects (unless you have to for privacy/secrecy/etc. reasons.)
- Number and/or date all of your pages. I date at the start of each day, and number all pages, although I don't date all the pages.
- Number your pages sequentially across multiple notebooks. This is nice for when you want to write a reference to a previous page, even when it's in an older notebook it's not a problem. I started doing that about 3 years ago, before that I'd start back at page 1 for each notebook. I'm at page 1947 right now, I think I'll be lucky to get to more than 20,000 pages before I die.
- A few pages in the back for a simple index is nice.
- Use ink, not pencil, and don't actually scribble out or erase, just a simple line through is good. Sometimes you want those wrong ideas after all.
- Put a Tile or similar tracker on your notebook. They are pretty cheap now, and losing your notebook can really suck.