At a basic level, there are three (somewhat) obvious ways to sort all these. First is alphabetical by title. Second is alphabetical by creators' names. I think these first two methods could work pretty well, and the only reason to prefer one over another is your personal focus. If you're a big fan of Batman, it probably makes sense to keep all the Batman titles together. If you're a big fan of Jack Kirby, it might make more sense to keep all the books that he worked on together. A third method would be to organize them all chronologically, but I think that would become awkward with more contemporary works where a single story might be spread out over several issues and, if you've got more than one monthly title you're dealing with, that could get challenging to keep straight.
Regardless, here's a quirk you immediately have to deal with if you're using long boxes to store your pamphlets: a lot of graphic novels don't fit in long boxes. Many do, and I've seen plenty of folks who store tradebacks in with monthly floppies. But many don't.
And going in the opposite direction isn't easy either. Sure, your typical manga can fit in a long box, but they're so short and narrow comparatively that you wind up wasting a ton of space. Not to mention possible damage to your floppies if they're pushing up against and start bending over the smaller manga.
I think many fans come to the same conclusion: that you just have to store them separately. Oh, sure, you could put your pamphlets on a bookshelf in and amongst your graphic novels, but it's much, much hard to sort through them since they (generally) don't have a spine thick enough to include any identifying information.
OK, so long boxes for your comics, and bookshelves for your grapic novels. Maybe a separate bookshelf for your manga, as you run into that wasting space issue on the regular bookshelves as well.
And here's another issue: oversized books. I've got about two dozen books that don't even fit on my largest shelves! Am I supposed to build shelves big enough for those books simply in order to have them alphabatized with my "normal size" graphic novels?
I was cataloguing and storing some books over the weekend, and I bemoaned on Twitter that I wish I had a library sciences degree to help sort everything. Carol Tilley (you know, the woman who debunked all of Wertham's bullshit last year?) engaged me a bit about how I could still go back for an MLS degree. She actually has a PhD in Information Science and, on top of her teaching duties, has a pretty active hand in library science journals and such. All of which is to emphasize that she knows more than a thing or two about library sciences. Do you know what she said when I noted I was having trouble with some obscure titles?
@skleefeld I think very little would help you in that quest. Ppl who do serials cataloging and management are wizards of the highest level.— Carol Tilley (@CarolGSLIS) March 28, 2014
You know, I used to scratch my head over comic shop owners who sorted their long boxes, as near as I could tell, by alphabatizing whatever the largest word on the cover of any given issue was. Action Comics would be listed under "S" and Detective Comics was under "B." After getting pretty sick of sorting this past weekend, I realized that I threw Alfred Bester's The Stars My Destination Volume 1 right next to The Complete Alfred Bester's The Stars My Destination. And both of them are listed under "S" despite the word "Complete" and Bester's name being part of the formal titles. I kind of don't wonder about those comic shop owners any more. After all, if folks with a doctorate in sorting exactly this type of stuff out can't figure it out, I'm pretty sure I'm not going to solve the problems any time soon.