Hey Nick.
Suggest that you read:
http://dranger.com/ffmpeg/tutorial04.html. Especially the section on aspect ratios.
Here is a relevant section:
Since our screen can be of any size (we set ours to 640x480 and there
are ways to set it so it is resizable by the user), we need to
dynamically figure out how big we want our movie rectangle to be. So
first we need to figure out our movie's
aspect ratio, which is just the width divided by the height. Some codecs will have an odd
sample aspect ratio,
which is simply the width/height radio of a single pixel, or sample.
Since the height and width values in our codec context are measured in
pixels, the actual aspect ratio is equal to the aspect ratio times the
sample aspect ratio. Some codecs will show an aspect ratio of 0, and
this indicates that each pixel is simply of size 1x1. Then we scale the
movie to fit as big in our
screen as we can.