When I started out, I think I somehow was under the impression that .emacs.d was some sort of cache, and not for end-users to mess with. Actually, I feel like when I first started out on Red Hat 5 it wasn't there, but I probably just wasn't being very observant.

At some point I set up auto-insert for a variety of files, and the howto I found used the directory .autoinsert, and at the moment that's actually where my elisp that isn't in my .emacs lives. It's a little hacked together and ad hoc, but not worth my time to fix. Nowadays I've customized everything I want to, and mostly am installing thirdparty packages.