It depends on your application. If you're making a server-side app with only modest javascript (less than 100kb minified) then go for total bundling, you're probably going to be fine.
But if you're making a javascript app and have a ton of code in it, then your needs are going to be different.
For example, in my app I bundle all the core files. There's jQuery, underscore, backbone, my main app files, my user login system, my layout system, my notifications and chat system, all are part of my big initial file.
But I have many other modules as well that isn't part of the initial bundle, that are loaded after those.
The forums, the wiki, the wysiwyg, color picker, drag/drop, calendar, and some animation files are part of the second category. You need to make reasonable decisions about what's commonly used and needed immediately vs what can be delayed.
If I include everything immediately I can get above a meg of javascript, which would be insane and make the initial boot unacceptably slow.
The second category starts downloading after initSuccess
event fires from the initial file.
But the second category is more intelligent than the first in that it loads what's more important first. For example if you're looking at the wiki it'll load the wiki before it loads the color picker.