Have you tried index cards now they have this digital thing where you can just slide all your papers into this machine and it will down load to your computer and organize it as well. It was on tv can't remember the name of though
I have a binder separated by tabs. The tabs are labeled poultry, pork, beef, main dishes, desserts, vegetables, salads, crockpot, miscellaneous, seafood, holidays. Probably not the most efficient way but so far it works. There are a few recipes that are real winners that I make several times a year and they are put into 3-hole sheet protectors to protect them while being using.
I have a bunch of recipes I haven't even tried yet and they are 3-holed punched and filed in the binder without a sheet protector.