I've only been playing this game a couple of weeks so other people have probably already thought of these, but I am proud of them anyway:
1. Really fast troop transports: if you have really fast engines on your troop transports, you can use them to invade planets in tactical combat that are festooned with numerous missile and point defense guns armed weapons platforms, just by zooming past the missiles when they are launched, and capturing the planet, and then the captured weapons platforms will shoot down the missiles they themselves launched with their own point defense guns.
2. Covert mine laying: create some long range ships with adequate cloaking and scanner jamming components and mine layers, and unassuming names (so human player opponents can't tell what you are doing). Then deploy mines above all the planets and warp points of your current allies. Then if they later decide they don't like you or vise versa, and break the treaty, they won't be able to get to any of their planets without sweeping the mines first, and they'll probably lose lots of ships before they figure this out (I wonder if newly constructed ships will hit mines above the planet where it was just constructed? Haven't tested that yet). I don't think there is anything they can do to stop you while you are treatied with them and they can't tell what you are doing until it is too late.