Mi dos centavos (which may or may not be helpful): Much of my physical collection is hopelessly confused. Maybe that's part of the fun, having to leaf thru zillions of issues to find anything specific, like browsing library stacks and encountering serendipitous neighbors. My huge DIGITAL collection is much better organized, because I don't have to find ever-more shelf space. My digitals are arrayed as:
* modern major US-UK publishers
* modern minor US-UK publishers
* vintage publishers, any nation
* 'underground' publishers, anywhere
* European (mostly French-Benelux) publishers
* Manga from any nation, sorted by language
* franchises and creators not tied to specific publishers
* 'other' sections for one-offs, webcomix, etc
My physical collection (or accumulation) of comics is heavily slanted. I have a large set of undergrounds, a fair number of Silver Age, some modern comics, very few Golden Age, and a smattering from Japan, Mexico, Benelux, etc. The few GA comics are mostly mixed with other illustrated magazines of similar vintage. The larger SA set are sorted by publisher and subject, so all the Marvel barbarians are together. The many undergrounds are mostly arranged by title or creator, so all the R.Crumb's are adjacent. Illustrated humor books get their own shelf.
And hey, if you think my comix collection is a mess, you should see my much larger accumulation of music books and sheet music! Guess I'd better scan the better covers before I donate the lot to the local high school music program.