Those folders are not WP's. Does anybody know about a plugin that would do something like that? Otherwise it's still a very serious hack. Have you checked error and access logs and found anything out of order?
Btw. We've talked about timestamps. Did you check what timestamp all these weird extra folders and their files had?
When you've fixed things, you still have to make sure there still not a hack file somewhere, or something in your database that shouldn't be there. Make sure to change ALL passwords (WP, database, control panel, etc.) and read the hardening wordpress text in the codex to try and prevent this for the future.
(Actually I'm still curious about the "how" of this hack.)