Black hole event.
A black hole appears somewhere in the galaxy, and it has a radius of 5x5 parsecs. Anything within this parsec is destroyed. Yeah even planets are erased from this cosmos, but stars are not. Each turn it moves off in a random direction until it either dissipates or moves off the map edge. This could really shake up the game, as ethics come into play. Do you spend alot of money trying to rescue your people in ivacuation ships, or just leave them to their fate. If its happening to another civ, do you aid them, or take advantage of the chaos and invade while they are weak? Does another civ? Also diplomacy, as you try and convince other civs to do their best to help you if they can. You can also try and get a ship outfitted with a black hole gun (if researched) to try and 'cancel out' the black hole, but it will not always be successful.
Robot Rebellion ala I, Robot.
Your/another civs industry is crippled until you can quell the robot uprising.
You have to cut off the (random amount) planet/planets that have rebelled then invade them and retake the planet. The planets are still 'yours' and no new civ comes of it, but those planets are doing absolutely nothing for you apart from sapping your economy.
'Tyranids' or 'space locusts'
Anyone here who has played, plays or knows about Warhammer 40,000 should know what I'm talking about. They are galactic locusts. They are a hive mind controlled race of bio-engineered insects and creatures who basically invade a planet, destroy it, eat everything on it and leave to another one. Of course the devs will have to think up another name that tyranids but the premise will be identical. The planet they invade (because they scour it of its atmosphere, its water, biological and non-biological matter and consume it) will be reduced to a class 0 planet. You can fight them, they have good soldiering ability, and ALOT of ships. They will invade randomly, and often invade one planet, float around, move the other side of the map and invade a planet there too. This idea sounds really cool, as you can (if you think you can benefit from it of course) leave them alone and see if they invade other civs, or try and destroy them.
Whats also cool is that they reproduce lost ships over time, so if left untouched after a big war they will end up being just as powerful as before.
1. Black Holes don't work that way. They have immense mass and gravity, they're most likely what holds a galaxy together, if they were able to move through a galaxy, it'd be destroyed, period. They don't work like Spheres of Annihilation in D&D.
2. I like the idea, but don't mention the movie I Robot.
Eugh. Better yet, why not make it like in Civilization: Call To Power, where you have an AI revolt. (Much like a Civil War.) And the machines and computers you once used as tools demand equal rights and become their own civilization, taking half of your techs with them.
3. The biological space locust thing has really been done to death. Zerg, Xenomorphs, Tyranids, etc. Not that it wouldn't be good to be included but I'm sure the Galciv Guys could think up a better version of this. As it is they just sound like pirates that attack with transports with extra cosmetic effects.
For the most part, good ideas though.
GalCiv2 Forums
Mega Events are a new feature in Galactic Civilizations II: Dark Avatar that look at the state of the game and then try to intentionally shake up the whole galaxy (they're optional). Now that some of you have been playing Dark Avatar for a bit, we'd love to hear what additional mega events you would like to see in the game. Comment here with your ideas and we'll look through them and add into the game some of the ideas! 
?! I know but its a good thing, maybe the planets been hidden with cloaking device or somethings, devs use your imagenation 
Sounds like you enjoy it a little too much. 