For a while, I tried to keep my RPG library alphabetical, first by game line, then by title; so GURPS came before HERO and GURPS Cabal preceded GURPS Celtic Myth. That worked pretty well, I thought.
Well, living situations changed and so did the number of and arrangement of shelves I had access to. I found myself keeping a large chunk of my RPG books on a shelf in my closet. Also, running a Mage campaign meant I referred to those books a lot, but they were all inconveniently located in the closet, since that was the only place that could house all of them at once.
Now, I've just set up something new. The top of my bookcase is now the space for whatever game I'm currently running. It's got all the books I find myself repeatedly using, or think may come in handy. So now, for the Mage game, aside from a best hits list of Mage, I've also got Unknown Armies, Suppressed Transmission plus a lonely Changeling book.
I also rearranged the shelves around the room so their contents are books I really like, or haven't read yet, rather than slavishly following the alphabet. This means the closet shelf is now a random hodge-podge of books in no particular order, aside from being alphabetized within a particular gameline.