I'm sure everyone's methods of organizing are different. We do what works for us and I am certainly not a very organized person! But I'm learning!
I like to have all the year's books at my fingertips, which can be difficult with a toddler who likes to keep her fingertips busy with all the books!
One of the things I started this year was "book baskets". I got this idea from My Father's World. I picked up some inexpensive baskets at my local thrift store and use them for my boys to place many of their reading books for the year. When my son is done with a book, I can just say, go check your book basket and he can find another book. Here is our high school book basket.