Digital sources; either my own or on-line.  Over nearly a decade I compiled most of DC & Marvel's classic wares, their biggest rivals, and the bulk of the major indies, from the 80s and early 90s; plus a pretty good selection of the Golden Age and 1950s.  There are gaps, but mostly just individual titles and more minor ones, at that.  Some companies, like Charlton, I have their main bread and butter, but not as much of things like their licensed tv stuff, or some of the stuff they picked up from other publishers; or, there are gaps in a run, like Fightin' Army.

The images I pull are from on-line, which is why some of them have gone missing, in past reviews.

Well, I was switching to book collections into the 90s (working for a bookseller helped) and sold off the valuable stuff in my collection, after obtaining a trade version, then donated the bulk to a friend, who volunteered at a childrens home.  I was pulling back from the market, anyway; so, trade was the way to go.  Then, around 2010, I discovered digital sources and was able to get entire runs of a comic on a single disc, or even entire companies (I have all of Atlas/Seaboard on one disc, except for the romance magazine they put out).  It was also a great way to compile Golden Age and more and more of that was uploaded to sites like the Digital Comic Museum, with legal, public domain titles.  

DC and Marvel are pretty much available through digital sources, Western/Dell/Gold Key is mostly (with some minor gaps), Heavy Metal, Warren, the Disney Ducks; EC, Archie's superhero and main line (with gaps on some titles that people keep filling in.  Charlton was a tougher one, as sources would have the Action Heroes and the horror titles; but, the war comics had gaps, as do the westerns.  People have slowly filled in the gaps.  I was lucky to find someone who had compiled the complete Lonely War of Willy Schultz, though.  My Hercules files are missing the later issues, though, as no one seemed to have those, which had Sam Glanzman's most experimental art.

80s/90s independents can be haphazard, like Vortex, for instance.  I have Mister X and a few of the other titles, but do not have the Vortex anthology.  Slave Labor is one I just have bits and pieces.  No one seems to have their short-lived Scarlet Thunder (about a pair of Golden Age speedsters) that I quite liked.  I have a pretty big collection of Dark Horse; but, no one seems to have The Mark, apart from the storyline in their Mayhem anthology.

When I was doing the Charlton retrospective, in my Other Guys thread, I got a lot of help from on-line blogs, like Rip Jagger's Dojo and The Charlton Library, for samples of individual titles I didn't have, plus the two issue retrospective that The Comic Book Artist did on the company, in the early 2000s.

I made the mistake of reorganizing my collection by alphabet last night. Completely on an impulse. What a mess.

Currently, I have most of the collection in alpha-numeric order by the title of the book. But there are exceptions that seemed logical when I started, and now it would be a major hassle to move them. My first box begins with titles that start with numbers (2001, 2099, 52, etc). If there are enough issues that I think they should have their own slot, I'll stick a divider with a nice label in front of the series. After the titles with their dividers, I make a divider for the misc titles. I pretty much do it that way all the way through, but.... For some reason, I had to have all my Avengers titles together, so every Avengers book that had more than a few issues is filed right there in my A's. For one shots and minis, there is a misc Avengers slot at the very end. Batman is similar to that, but every Batman title with it's own divider starts with the word "Batman". All of the main characters who have tons of different minis over the years each have a divider for "Misc" (Spidey, Cap, Iron Man, FF, Batman, etc), and there is a misc divider at the end of each letter of the alphabet. However, the Z's aren't the last comics. I have 8 longboxes of Superman titles from the Golden Age - 2011, and the way I have them arranged is unexplainable (but it makes me happy that I've made some sense out of a very confusing continuity). At the very end of the collection, I have my FCBD books, assorted previews, and lastly magazines & digests. Over 42,000 in all, in order, with easy access to any book, anytime.

Sounds a lot like my system, or what it will be once I'm finally done reorganizing.

I'm many years overdue for re-organizing my collection. But a large bulk of it, I started with Marvels, series filed by the date they started. So, for example...

FANTASTIC FOUR
HULK
ANT-MAN
THOR
IRON MAN

...and so on. Crazy, I know, but, it works for me!

Smaller, independant publishers, I tend to put each publisher alphabetical. The exception is series that go from one company to another to another, then everything of that series is together. Ditto with certain writers / artists. I currently have 3 entire short boxes filled with nothing but Edgar Allan Poe-related books... most of which I never had or even heard of until 5 years ago.

There's only a handful of characters for which I have lengthy runs, or decent-sized multiple runs. These guys get their own space on the bookshelf, and the issues are sorted in-universe chronologically, regardless of title. Everybody else gets put in the catch-all company universe sections, also sorted in-universe chronologically. This probably sounds like a mess to everybody else, but it makes perfect sense to me, and with these sections documented in web pages, it's easy enough to find an individual issue, especially since about 80% of my collection is collected editions now.