How to Set the defaults for Render Queue in After Effects
I'm pretty sure it hasn't changed since CS3 (in fact It's been the same for as long as I can remember): in Edit &gt; Templates &gt; Render Settings &gt;. Another way of getting to this dialogue is from the Render Settings drop-down in the render queue. At the bottom of the list of templates in the drop-down is Make Template… 

Choosing that brings up the dialogue box pictured below. Up the top of the dialogue box you'll find Movie Default; set that to whatever template you want to be the default for renders. If you haven't got a template that has the settings you need then you can make one here - hit the New button, set all your settings and give it a name.  I find duplicating an existing one and modifying it a useful way to go.

Same goes for the output modules, which you get to from Edit &gt; Templates &gt; Output Modules, or from the Output Modules drop-down in the render queue.