In non-fiction, you should organize the things you find in your research in a way that will make the most sense to the reader. History books aren't always strictly chronological. Often they will cover some sections thematically or regionally, depending on what they are trying to get across.
Now, on to fiction -- I have mixed feelings about the Harry Potter books. Sorcerer's Stone is absolutely fabulous. Unfortunately, the sequels follow the rule for sequels: At best, a sequel can only be ninety percent of the original. By the time you get to book seven, you only have thirty percent or so left....
However, from what I understand, J.K. Rowling had written out the basic structure of all seven books before she really finished the first book. Since the plot is fairly complex and involves a large number of characters, this is very important.
I have to write from an outline. I don't always write it down, but I have to have a structure. In college, I got about half way though writing a novel and discovered that the turning point of the novel depended on a character doing something they would absolutely never do. (In retrospect, there was a whole lot more wrong with the novel than just that -- but I never could figure out how to write myself out of that corner.)
I read about another option for script writers in The Writer's Digest: create all the scenes you think you'll need and put each on an index card. This way, you can arrange them in multiple orders to see what makes the most sense.
So, before you start writing, be sure you know who your characters are, what their secrets are and how they will interact with the other characters. What questions can you ask at the beginning of the book that will keep people turning pages until the very end? Obviously, you don't want the action to peak too soon. I love the Lord of the Rings books, but the scene in Moria where Gandalf confronts the Balrog is difficult to top and it happens in the first book of the trilogy.
In Peter Jackson's Return of the King they saved much of the "Falling Action" for the Extended DVD, but the movie was still roundly criticized for taking so long to get to the closing credits. But they did audiences a much bigger favor than the original novel. The high point of Tolkien's Return of the King happens in the middle of the book and the "falling action" takes a very long time to get through. (It's important. It shows how much the characters have changed. Tolkien scholars will tell you that the return to the Shire is probably why he wrote the book to begin with. But it's still falling action.)
So, try to plot out your book so that the reader will feel the discomfort of unresolved conflict until the final chapter. If you feel there is some important aftermath, try to be brief. Rowling sums up the destinies of her major characters in a few pages. If you can't be brief, then save the aftermath angst for the beginning of the sequel. (Possible spoiler here...) Personally, I'd love to know what happened to Frodo when he got to the undying lands of the Valar. After all, if you read the Silmarillion (and I don't suggest that you do) that's where all the evil in Middle Earth came from to begin with.
One final note about creating an outline: be careful who you share it with. First of all, your notes may not make any sense to anyone else. Second, some writers worry that if they tell the story to someone, their pent-up story-telling energy will be released and they will not ever be able to get it on paper. I don’t know if that’s true, but I have discovered that some of my stories become less “urgent” to me when I’ve told someone else about them. My wife and I wrote Broken Toys: China’s Song together. I would scratch out the first draft on a legal pad and she’d type it into the computer. I stopped comparing what I’d written to what she’d typed when I realized how much better her typed version was. (We both spent a lot of time going over the second and third drafts together -- but that's another post.) However, if my memory serves, I didn’t tell her what was going to happen next in the story until I’d written it – which drove her crazy.