edit: this is totally Thelogan.
My old man organizes by some weird artist/writer/inker system, I never liked it. He seems to be able to find anything instantly, but I submit this: What if the writer and artist hold equal merit? I don't want to make those kinds of calls.
My longboxes are meticulously alphabetized, so Amazing Spider-Man is in the "A's". I don't do that with the shelves, Astonishing X-Men and Uncanny X-Men both go in the "X"'s and then get sorted chronologically.
It's a good system, dammit. If my shelves were a store you would be able to find what you were looking for quickly with no previous knowledge of Omnibuseses or Marvelses.