Alphabetically sounds like the way to go. Perhaps there should be a section for weird packaged items to, that can't necessarily sit amongst normal CD cases and tapes cases. I've got a lot weird packaging stuff in collection and I've designated specific boxes for those anomalies, but yeah Discogs can be good and bad I think. I started to catalog my collection late in that game, so it's hard to know what I've missed from the time I started. It's an interesting way to keep track of things you have, but it's not a perfect system either. It's kind of a scattered mess of sorts.
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Special packaging can be a dilemma. A few of the things that fit, I'll put on shelves. At least with CDs, though, unless its holding the CD in something equivalent to a spindle, I remove it from the packaging and put it in a blank jewel case so it doesn't get damaged. I try to place all those "special packaging discs" on the shelves at their proper place in my system, but that's where I do have to be careful, especially if there's no real identifying info on the disc itself. Its easy to put them out of place. But again, if everything else is organized, you can track down the "rogue" items fairly easily usually.
The packaging itself I have several storage bins where I've put all that. No real organization or cataloging there. I figure if I ever have to pull any of it out for a sale or whatever, I'll just have to dig a bit. At least I have a general idea of where it is. I never throw anything out, so I know its there.
Yeah, the chronological ordering is certainly not ironclad by any means. I mean, if I've got 8 Merzbow CDs from the 95-97 period, it really doesn't matter if they're all in the exact order they were released. But I know exactly where to go on the shelves to find mid-90s Merzbow CDs with how I've set things up.