Blogger Adam Gurno has shared his system on bookmarking books using post-it flags. He calls it vertical cross-reference. Sounds like a complicated idea? It is not:

… Before I run off to write the code, I’ll take 15 seconds and put a set of same-color flags near the XmFree in the index, the XmFree page, and the radio button page, and I will line them up. So the next time I hit the reference book, if am reading a section that contains a flag, I can tell in an instant that I’ve been there before, which sections I’ve marked as ‘related’, and that I’ve found them useful in the past. This is a huge time saver, especially when faced with large, dense reference manuals. The flag are bread crumbs – path markers that you can trust…

In the simple words, this is a context based system. When you find a related topics within the book that you will reference later, you line up the flags and stick them on the side of the book. Later when you found one of those pages that related to the specific topic, you can immediately use the lined up flags to find the same or similar topics.

GTD: How to use Post-It Flags – [Just A Guy]