First off, as you noticed the numbering is worthless sadly although from all the different companies I've seen this seems to be common!

I organize my books thusly: I separate Wizards products from all the others. That way if I want (or have a DM) who only allows core D&D material it's easily identified on the bookshelf. I then break down the books by uses. Is the book aimed towards DM's, players or a campaign setting?

It can be a bit hard to parse which books are DM focused/player focused as some of them are sort of up the individual owner. I usually divide campaign settings the same way.

I tend to organize my other supplements by company and then line/setting.

First off, as you noticed the numbering is worthless sadly although from all the different companies I've seen this seems to be common!

This is how I organize my D&D books: I separate Wizards products from all the others. That way if I want (or have a DM) who only allows core D&D material it's easily identified on the bookshelf. I then break down the books by uses. Is the book aimed towards DM's, players or a campaign setting?

It can be a bit hard to parse which books are DM focused/player focused as some of them are sort of up the individual owner. I usually divide campaign settings the same way.

I tend to organize my other supplements by company and then line/setting.