I would archive the magazines in clearly and detailed-ly labeled boxes assuming you won't have need of them in the near future. As for large items, could you not file them in a bin of some sort? I have in mind the way poster prints are displayed in arts and crafts stores such as Michael's and Hobby Lobby. If you don't have any bin to put the things in, perhaps you could make a simple one out of plexiglass or perhaps they would stand up on their own and you could "file" them against a wall. I think that you are clinging to the concept of filing reference material in file folders. This is the way The David talks about reference. But he apparently doesn't have printed graphic design projects knocking around to deal with. The thing is, you need to know where it is when you need it. A file cabinet is convenient and a logical way to achieve this with bits of paper, but there's nothing saying you can't have your "large reference" file against the wall or in a closet as long as it works.

I have a ton of books from school, which I consider reference material. This includes photocopied coursepacks of readings and other smaller things. If I were to have the same "problem" that you are having I would be trying to file my several hundred page books in file folders, which just doesn't make sense.