Ok guys since yall are the WORLD’S GREATEST FANS EVER, I can think of no better place to go to aid in my dilemma…
So, due to my recent anxiety over my fear of DC being gone BEFORE coronavirus, I have recently been trying to redo my DC Library, as I have collected many, MANY more singles, TPBs, Encyclopedias, Guides,etc. Problem is,I have NO IDEA how to organize them. I tried Cononical Order,Pre/Post/Beyond Post crisis, Earth Designation, but everytime I try, there are certain books, or series that throw a monkey wrench in the whole operation. I am now at the point of RESTARTING IT FOR THE 5TH TIME IN 2 WEEKS! I’m about ready just to go alphabetical, like comicstores, but this will present even its OWN set of continuity issues. Any suggestions? I’m seriously losing my mind here!! (ALTHOUGH a part of that may be this whole RONA-mania we’re experiencing, while the MAJORITY is of my fears that we may lose DC one day here coming up the way things are going for us DC-ophytes).
DC Comics aren’t going away any time soon. As for how to organize your books, well… everyone has their own system. There’s no right or wrong way to do it, just use the best system that works for you. If basic alphabetization bores you, maybe try grouping them by character!
I use basic alphabetization. It’s easy to remember and you don’t need to clog up your mental sponge (brain) with all manner of “Silver Age trades here, Modern Age resource books there, books by so and so over there”, blither-blather that can potentially confuse you and make you feel like you have a big, unintelligible mess that can never be organized in the long run.
Just A-Z, easy-peasy. 
SN: Numerical titles (such as 52, among others) can be alphabetized, but I always put them before other books. Numbers first, then letters.
I split it into 3 factions. All of my Runs, Graphic Novels, and Single Issues are divided into my Batman Timeline, Masterpieces Collection, and Historic Comics. My Batman Timeline is the complete history of the character in the Post Crisis Continuity. The Masterpieces Collection is single issues, Graphic Novels, and Runs that are works of art and considered great. Historic Comics are Graphic Novels, Single Issues, and Runs that are important for comics as a whole. I hope this helps you come up with a few ideas.
This is probably the closest to how I TRIED to organize my books before my recent attempts. And it was a great way of doing it. My issue, ultimately, was that I have been lucky enough to find some floppies of some of my favorite storylines (all having been put together in GN format through TPBs.), as well as tie-ins, which became the main thorn in my side!! So, let’s say I’m reading All Star Squadron, but 2 issues tied into Crisis. My All Star Squadron section would then have 2 issues missing, as I would try to organize the tie-ins with the main story lines of Crisis in the order they are supposed to be read. However, when I tried organizing by alphabetical means (by comic titles), one would have to go from Crisis, then find the next one in All Star Squadron, then jump to, let’s just say Batgirl, then go find the next comic in the series, amd so on and so forth. But I think I’m gonna go this way (or at least START this way until I hit another wall!
Think of it as a large TV series, You have your leads and other favorites. You want to make sure they are fleshed out before the big crossover.
Some things I kept in mind as I organized my comics:
-Do I need this to make sense to other people, or just for myself?
-Do I care more about a consistent, logical order or ease of accessing my favorite books?
-What are the limitations of the physical space I’m using?
-How much effort do I want to spend maintaining the organization as my collection grows?
For my books, that worked out like this (for now):
Everything is organized into Pre-New 52, New 52, and Rebirth. In each of those sections books are organized by character group (i.e Bat Family, Flash Family, Titans), then chronologically by series start date. Special events (Countdown, 52, Flashpoint, etc) get their own section, with the exception of tie in issues that happened during a book’s normal run (like most of the Our Worlds at War and Final Night tie ins.)
Good luck!
What I’ve tried to do in the past is organize it by alphabet, but with some of the big characters, I’ll separate the continuity books from the more prestige books. So for example, with Batman, stuff like the Grant Morrison, Scott Snyder, and Tom King runs are in chronological order, and then after that you get books like Miller’s Dark Knight books, Batman: Damned, and stuff like that.
Hopefully that helps. 