By the way the Quake "pk3" format does not really make the game harder to "hack", you can tell your system those are zip files and suddenly you can browse them like normal folders.
Indeed. In fact, the pk3 format is one I was thinking of in particular, as well as what the Unreal engine uses, etc. In some cases, though, they are a custom format and aren't so easily opened. But that's beside the point of my question.
I was thinking more in terms of organization, where instead of having folders that are basically art/music/asset dumps, they're more organized.
There's another engine I've used that utilizes a kind of "virtual folder" system which I really like. Outside of the engine/editor, it looks like a single file with a custom extension. Inside the editor, though, it's an entire hierarchy of folders and files the engine uses. I suppose it's effectively like having an entire folder hierarchy archived into a single file, which is then opened by the engine/editor. Whatever the mechanics behind it, it's a cleaner, more organized presentation that I really like.