Binder guy here:
Corp binder: all IDs up front, then sorted by faction, then type, then set, then numerical in set.
Runner binder: same
One binder per faction, all IDs up front, sorted by type, then alphabetical (at 8+ data packs, I'm already thinking organizing by set is not providing a lot of value. It was nice when I knew which set things were associated with, but the card volume is enough now I'm thinking more in terms of card name than set name). The downside of this, of course, is that every time a data pack comes out I will have to redo just about every binder page. So we'll see if I stick to this or not.
I do have a friend who just does straight alphabetical across the whole thing, largely because he builds decks using online tools so that sorting order helps when it comes time to actually build the deck.