My system is not perfect I still spend way to much time looking for specific images, But it has evelved into a pretty good system. I file all negs in neg pages marked and sometimes dated. They are all filed in oversized three ring binders that are started new every year by catagory. I/E Landscapes 1998 or Nudes 2000 or street shooting 2004. With every page there is a proof sheet and a note page.
These binders are kept on book shelves in a dark corner closet in the darkroom. Well protected from the environement yet easy to access (though I am running out of room).