I have one favourite pen that follows me everywhere and all the rest of my stationary lives in a small tool/tackle box with heaps of compartments. Seems to fit everything in neatly and sits on my desktop. This is a remnant from a graphic design course I had started, for which we had to carry an extensive set of pens around with us all the time. I don't take it with me anywhere now but I still find it useful for keeping everything in one place. I had considered getting a proper stationary organizer but none of them seemed just right to me either.
I Don't know how well it would work for anyone else as I am a student and only have a home GTD setup so don't have the same type of environment as those working in an office might do.