You may want to look at ShrinkSafe and the Dojo build system. While it does not create quite the compactness of the Closure compiler it does get you close without enforcing constraint on the way you write JS.
As well, if you are doing large apps with jQuery then you should take a look at Backbone. It helps organize the JS application architecture. In saying that though there really are better toolkits for large JS apps that are designed to provide the frameworks of application architecture in your app.
Dojo is the one that I use and recommend, once over the learning curve you will find that it is designed to handle large JS application is an intuitive manner and not just by making it look like Java in the browser. It exploits the best parts of Javascript while bringing in language constructs from several schools of thought to provide a very robust toolkit.
I have used most all of them and it is my choice when the webapp surpasses a certain point in complexity. I always tell people that I can save them a lot of time when it comes to JS toolkit selection and then I tell them if it's small use jQuery and if it's large use Dojo. It is meant to be slightly humorous but there is a grain of truth to it.
There is nothing faster to learn and more intuitive that jQuery but it comes at the cost of reduction in it's robustness. There are tools to address this but to me they always feel like bolt on's.
Dojo on the other hand trades up front intuitiveness for robustness. A trade off that toolkits like Closure make is to make JS more like Java to bring back some of that intuitiveness but at the cost of some of that robustness. Dojo is unapologetic a JS toolkit and uses JS concepts as first class citizens. It then borrows best of class language constructs from other areas of language progression.
Anyway, my long winded point is, if you are having issue with growth of your jQuery application you may want to give Dojo a try. Rebecca did and was pleasantly surprised:
http://blog.rebeccamurphey.com/2009/11/12/dojo-confessions-o...