As a pet project, I am trying to get familiar with NodeJS and CoffeeScript, and am finding it hard to get the ball rolling.
I've found plenty of examples of single-file super-simple apps like in CoffeeScript's examples folder, however, none of those really show what a full application would look like. I've also scrounged Google to no avail.
Do you have any examples of medium-sized, multi-file CoffeeScript/NodeJS apps I could learn from?
See this gist: https://gist.github.com/652819
Its pretty much an entire NodeJS app using the Express framework, Redis for session storage, Couchdb as the database and written in CoffeeScript. However, you are asking for code organization. That depends from developer to developer. I personally prefer Express. However if you prefer MVC style then see Geddy.
GitHub is your friend:
And if you want even more, take a look at the listing for the Coffee-Script Language. I suppose that 95% of the projects there are related to Node.js at the moment.