I think the file structure from the Discover Meteor Book is really good and a solid start.
/app:
/client
main.html
main.js
/server
/public
/lib
/collections
- Code in the /server directory only runs on the server.
- Code in the /client directory only runs on the client.
- Everything else runs on both the client and server.
- Files in /lib are loaded before anything else.
- Any main.* file is loaded after everything else.
- Your static assets (fonts, images, etc.) go in the /public directory.
