This story is entirely different for IE. While most of the core API such as
String are the same, IE differs greatly when it comes to the
document object, and any manipulation therein I would agree with balexandre and say that jQuery does a very good job at taking care of that mess for you.
If you write a jQuery app, you don't need to worry about anything as you are developing to a framework/library that does (today) and will continue to do (in future versions) everything under the hood.
as you need not to develop your app in one browser but to test in all other browsers, and simples things as opening windows and handle ajax calls vary from engine to engine...
so... please keep aiming to jQuery :) he will do the hard stuff for you ;)