Perhaps because it's written with examples in java but I often feel like no one in the rails community has ever read Eric Evan's Domain Driven Design[1]. It's far and away the best material I've ever seen on how to organise large code bases. It covers pretty much every suggestion that I've seen from the rails community. Sometimes the rails community can feel like the fitness industry, everybody just rebranding things that have been done before.
[1] http://www.amazon.com/Domain-Driven-Design-Tackling-Complexi...