I have two paper organizing systems--one for stacks and one for sheets. After I've finished using a stack for a particular project I rip it up and sort into drawers split by color. I make a lot of themed minis and art journals, so I tend to exhaust most of a stack by the time I'm finished with a project. Stacks I haven't used go into their own drawers, very simply split into themed and un-themed. If I need Halloween or wedding or whatever I'll open the themed drawer. If I just want a fresh stack of coordinating paper I open the other drawer. I ruthlessly discard any stack sheets that I'm not fond of when I'm sorting remainders into drawers.
The only theme exceptions I make are for pets and Christmas. I sell/give away pet mini albums, so I keep all of my pet products, including paper stacks, dies, stamps, embellishments, etc., in one bin. Ditto for Christmas, but those stacks and products are dedicated to card and tag making.