I mentioned that as well. It's still in "reading order" but it goes by storyline.
For example, the pre-Infinite Crisis run. Action Comics, Adventures of Superman and Superman each had their own 12-issue arc in 2005-ish; they all ostensibly took place roughly around the same time in the DCU, but they didn't cross over much and can more or less be read in any order. So I just put them in the box grouped together - the 12-issue Action Comics run, then the 12-issue Adventures of Superman run, then the 12-issue "For Tomorrow" run in Superman.
That's how I arranged all the Superman (and Batman) books once they stopped doing "triangle numbers" or integrated stories. "This 6-issue Batman arc, then this 6-issue 'Tec arc from the same year, then the next Batman arc, then the next 'Tec arc..." etc. etc.
One-shots, mini-series and Annuals, I sometimes have to guesstimate where they'd fit but I'm always pretty close. If it's an Annual which has no connection to canon, I just put it in between stories by cover date - most DC Annuals used to come out in Summer, for example, so if it had an August cover date I'd put it in front of the August ongoing issues, unless the August issues were in the middle of an ongoing storyline, in which case I'd stick the Annual in right after that. If the mini or one-shot is blatantly non-canon, it would go in the "Superman - Misc." section which is after the ongoing series stuff.
It works better than I'm explaining it. But again, pull out any storyline from "Maximum Carnage" to "Death of Superman" or whatever, it's all in "ready-to-read" arrangement. Which is for me the most important thing.
Long, long, LONG time ago, when all I had was Superman and Batman stuff, I did just put stuff together by title. But I got sick of digging around whenever I wanted to read "Knightfall" or "Death of Superman" or whatever, so I finally just put everything in reading order and it's been that way ever since.
There's no real "right" way to do these things; the important thing is just that you know where stuff is when you're looking for it.
I also put "The Dark Knight" and "The Dark Knight Rises" with the rest of my Batman DVDs, even though they start with "D". Because they're Parts 2 & 3 of a trilogy, and the first movie started with the letter "B". Fight me.
