If front-end MVC Is too much for a given use case, then Twitter's Flight.js[1] seems like a great way to keep jQuery well organized. It defines a way to write jQuery components that communicate via events, piggy-backing on the DOM's event propagation. Quite simple, and ideal for when a single-page-app (e.g. the kind you get with Backbone) isn't quite right for you.

[1] http://flightjs.github.io/