One Small Square: Backyard. Would that go in Science or Literature? I also have Who was Helen Keller? - would that go in History (because it's a biography), or Literature? Another example - If Your Name Was Changed at Ellis Island - History or Literature? One more example, If You'd Been There in Bible Times - History or Bible?
Literature is for purely fiction. So here is how I'd catalog the above books...
One Small Square books are in biology (with other biome books I have)
Helen Keller would go in biography
Ellis Island would go in history & actually I have about 15 of those books so I'd probably just keep them all together (most are American history anyway)
If You'd Been There in Bible Times - Bible (just because my children would know to look for it there with Biblical maps, Archeology type Bible books, etc.)
The thing is to organize them according to how your family will best remember their location. That's the important thing.
Now
LibraryThing. I don't use any of the "discussion" features. I use it simply to catalog my books. You can upload 200 books for free (at least it used to be that way). I bought a life time membership which I think was only about $20. You can enter books by ISBN # which makes it really fast. I don't enter every single book. None of the ones that go in and out of the house quickly get entered. My primary uses for LibraryThing...
1. It provides a central location for a master list. It's great when my mother-in-law wants to buy hubby a book. She can look and see just what we have and what we don't.
2. It allows me to tag my books. So
Leah's Pony by Elizabeth Friedrich is stored in picture books but it is tagged with Picture Book, Great Plains, Great Depression, Dust Bowl, Horses, etc. So when I'm hunting up books on the Great Depression, I can click on that tag and all the books I have with pop up.
Katy and the Big Snow by Virgina Lee Burton is labeled Picture Book, Transportation, Winter, Snow, Boy Interest, etc.
3. The list can be accessed from remote technology so you can check for duplicates. I can be standing in the Goodwill bookstore and check to see if I already own, "Katy and the Big Snow." Look it up. Okay, I've got it already. Not such a big deal when you don't have many books but once you get thousands it becomes harder. Or when your hubby loves Louis L'Amour and they all sound the same to you. LOL.
Hope that helps. LibraryThing is definitely not necessary and it won't make your physical books any more organized.
Wife of 18 years to Jon.
DragonFly (12yo)
Buttercup (14yo)
I have a few questions - probably silly ones - but ones I need to ask. Do you put all picture books/chapter books in the "Literature" category? For example, I have One Small Square: Backyard. Would that go in Science or Literature? I also have Who was Helen Keller? - would that go in History (because it's a biography), or Literature? Another example - If Your Name Was Changed at Ellis Island - History or Literature? One more example, If You'd Been There in Bible Times - History or Bible? 
That makes total sense and clears up some organizing questions I was having. Thanks - back to the books...