For more advanced stuff, your best bet is Prototype.
Dojo, YUI (and ExtJS, not on your list) are good if you have a massive team of JavaScript developers and need standards and solid documentation, but are overkill for 90% of projects.
Ext has a nice DataStore object for accessing remote data. And Ext has all those great "rich" components. But I found it wasn't much more work to do my own components in jQuery. (Tree is very simple to implement in jQuery from scratch)
The sense of control I have with jQuery is nice.
The main code to handle my own trees:
_.fn.toggleTreeNode = function(animate) {
var node = this.filter('button');
if(animate) {
node.siblings('ol').slideToggle(animate)
}
else {
node.siblings('ol').toggle();
}
node.parent().toggleClass('closed');
};
My favorite thing about jQuery is it makes doing things the right way very easy.
There's a lot of jQuery love and Prototype hate out there, which I don't quite get. Both are fantastic; both are bloated.