The jQuery Divide:Understand where jQuery ends and JavaScript begins

backbone.js is good. That gives you a fair idea about structuring your application. If you webapp is designed in a RESTful manner, backbone.js maps quite nicely to your backend.

There is also anecdotal evidence that jQuery qua jQuery has some fundamental limits. I worked on a largish jQuery application, written by ninja badasses, and it creaked a lot more than it should have for its size.

Comparable systems built on YUI seemed to have more structure. I actually went through the exercise of converting a prototype from jQuery to YUI3, and spent a lot of time working out their respective "philosophies". (see http://jsrosettastone.com)

There are newer frameworks (eg JavelinJS) that aim to be to jQuery what jQuery was to other frameworks.

I absolutely hate the plugin system simply because you cannot easily get the instance of the plugin an refer to it later. To answer this I use function constructors with the module pattern (its easy and doesnt require an extra lib to get going) to create my plugins. Another thing that I do is when I query for a collection of objects, create an array that represents every item in that collection already wrapped with the jQuery object. This may not seem like a big deal, but there is a difference between

    var collection = jQuery('a');
    collection.each(function(i, l){
        var link = jQuery(l);
        link.bind('click', function(){//do suff});
    });

    var collection = jQuery('a'),
        collected = (function(){
            var c = [];
            $.each(collection, function(i, item){
                c.push(jQuery(item));
            });
            return c;
        })();

Anyway, that is just a few ways that I use jQuery to make javascript a bit easier. These little tricks have the people that I work with thinking that I'm some sort of genius.