- /core - All files provided by core, that doesn't have an explicit reason to be in the / directory. More details futher down.
- /libraries - 3rd party libraries, eg. a wysiwyg editor. Not included by core, but common enough to warrant inclusion here.
- /modules - The directory into which all custom and contrib modules go.
I've seen some Drupal module developers out there have a lot of trepidation about moving to Drupal 8, most often via hearsay from others or via occasionally dipping in to look around and being spooked by newfangeldy stuff like namespaces, object-oriented code, and weird directory structures.