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mine are all in plastic sleeves in 3 ring binders.. 12 mags/1 year per binder.. organized in order sitting on bookshelves library style. Makes it real easy to get to any particular issue and to see what I have and don't have.
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I have the same set up as Ed. Mine are in five inch, three ring binders. They hold twenty-four magazines nicely. The magazines are stored in plastic sleeves from Office Max or Staples. I put mine together in two year increments. With my Hi-Po cars and Speed and Super Cars, those are broken up into brand specific binders while others are grouped by category like "drag racing" or "vintage speed part catalogs." I was never a fan of the plastic tote boxes because I reference and read my vintage magazines on a frequent basis.
Ed, post pictures of your library