So, this is something I'd really like to see: The ability to build "Interplanetary Missile Silo" improvements on planets.
This improvement would allow the planet to (with some kind of firing cost/delay between shots) fire missiles at other worlds (possibly with some kind of range limit, but it would have to be a big range to be useful; maybe upgraded levels of the improvement with stronger missiles/better range?). The missiles would move across the galaxy map at a certain speed, on auto-pilot towards their target, and could not be given orders. Upon reaching the target planet, the missile would impact, killing some amount of the population, destroying improvements, and possible reducing PQ.
Countering the missiles would involve sending ships to attack and destroy them mid-flight.
Of course, to be useful, the missiles would have to be resistant enough to being shot down to have a chance of hitting, but weak enough that you can't freely strike at well-defended planets. One possibility is to make them relatively fast, so only ships would good engines would be able to intercept them. You could also give them some level of weapons to defend themselves.
Alternatively, you could make them "Cloaked", and only detected if they came within a short range of something, or possibly only detected by Starbases with a certain level of sensor upgrades, and by ships with Survey modules (since I am all for Survey Modules becoming more useful).
There is also the question of how the missile would be affected by the presence of a garrison in orbit around the planet... (My thought would be to make the garrison auto-attack the missile IF a Fleet manager is built on the planet, since that's another thing I want to see become more useful)
Anyway, this was just a random idea that I'd love to see implemented.