It's nice to know someone else shares my obsession with books! You can't just get rid of them once you read them, I definitely can relate.
There are actually many ways to organize books. If you have an intensive collection, you might consider using a library classification system but most home libraries don't require such.
Many book collectors organize their books by subject while others organize them in alphabetic order using the author's last name. Others may choose to organize their books by size (which doesn't make sense to me) but if it works for you, go for it.
I organize my books by the type of book. I keep my resource books (dictionaries, thesaurus and such) in a shelf in my hutch on top of my desk right along with my frequently consulted business books on organization.
On my book shelves, I've organized my books by the type of book that they are first, and secondly in alphabetical order by author or subject.
For instance, one shelf contains non-fiction books organized by author; another contains fiction organized by author followed by self-help books organized by author. And I still have my college books which are organized by subject on a shelf of their own.
My cookbooks have their own shelf but they are organized quite differently. My favorites are kept all together with the rest of them arranged by the type of food that they contain. Check out my cookbook and recipe organization page to get a few ideas.
Magazines can be easily organized by subject using magazine files.
It is most important that you are able to find the books that you are looking for when you need them. Try a method and see if you like it. If not, you can always reorganize them to fit your needs.