Hi,

> Besides the obvious things of having a stable, clean power
>  supply with decoupling, good ground plane, short interconnects, and
>  low-pass-filtering the ADC input to limit noise and alaising, what else do
>  I have to watch out for?

I was involved in similar project for a club using an experimental rocket.
If you use low-pass filtering don't forget that an accelerometer can produce
high pic during the fly and then you can lost some informations.
Use a large piece of copper as ground for all pcb, prefer one pcb then
several, use balanced line for low level signal, put your accelerometer near
ADC, and... good luck !

SP