Some of the formats you can use are: an electronic file on your computer, such Word, there are new online services that allow you to fill it in as you write, and you can leave the story bible open while you work on your novel.
Here is a list of methods I've used:
Character profile: everyone from the main character to the waitress that serves your character's drinks.
I am a visual person, so I write down their physical characteristics, such as hair color, eye color, etc. I also treat them as though they really exist - where do they live, what is their childhood history, relationship with their families (at least for the crucial characters) what makes them tick, such as are they materialistic, or do they wear the same clothes on an almost daily basis. What kind of education do they have, high school, college, trade school, etc. if/where they work. Are they are in a romantic relationship? Do you want them to be?
One of the most important character profiles for me was why does my antagonist behave the way he does? What his his childhood like?
Next I wrote about the setting of my book, in the Pittsburgh Pennsylvania area. Since I used to live there, I know which ice cream shops and restaurants to send them to. I even printed out pictures of homes I want my main characters to live in. :)
Potential plot conflicts are another important area for me: should my villain attempt to kill off my protagonist and anyone who gets in his way, or not make him too evil. Making this decision in the beginning helps keep me focused if I'm not in a 'mean' mood. What conflict should I include for my both the protagonist and antagonist? I think of some ideas and write them in my developing scenes outline. Each chapter had a general outline of what needed to happen, but I was free to add in additional scenes.
My story bible also holds some words I looked up in the thesaurus so I could think of different ways to write walk, and talk. My binder is large so I can add additional bits of information when I find it.