I’m using C4D here for the Mograph tools. I might be able to achieve the same effect in AE, I’m just less familiar with it. Here’s an example of my end goal (though with a different size, scale, and undesired AA):
https://dl.dropboxusercontent.com/u/9144872/pixel-render.mp4
Here’s a zip with two example scene files:
https://dl.dropboxusercontent.com/u/9144872/pixel-dos-test.zip
In pixel-dos_no-tex.c4d, I’ve set up a 640×480 render. I’m cloning a grid of 8×16 blocks with random colors. The render looks close, though some rows render at 17 pixels tall, rather than 16. You can spot the difference if compared against the included pixel-grid-refence.png. If you hide the cloner and render pixel-grid-refence.png on one 640×480 object in the scene, it renders fine and the pixels exactly match that reference.

In pixel-dos_tex.c4d I take it a step further and put textures on all of the clones. In this example any of the 16-rendering-as-17 pixel tall rows appear to have their textures stretched to fit, resulting in random horizontal 2 pixel repetitions. (It looks like Creative Cow resizes my embedded images here, so you’ll want to view them full-size for the correct scale.)

My assumption is that if I could get the 16 inch tall objects to all render at 16 pixels tall, I’d have what I want. The interesting part for me is that one 640×480 object with a texture renders correctly, but a group of 8×16 clones that add up to 640×480 don’t. *shrug*