Space Crystal, or other gigantic alien lifeforms would be a nice addition. (Thinking back to my old MOO days). Incredible powerful entity, with huge attack values that destroys all planets/ships it comes near. Must move slowly.

Meteor Shower, X weeks until a planet blows up (possibly instead of just having a planet go boom seemingly randomly), with the possibility to build enough ships to defend a planet from the meteor/asteroid.

To Shadow, you could call that "Galactiga Ultimatium", for the Dark Ages, as that's basically what happens to all the empires with the near-reset effect, and lost technology. Could even add the possibility for the lost tech to be re-discovered/researched at a faster/slower rate then it used to.

I'd like to see technologies that can't be discovered through research possibly happen through Megaevents.

Supernova's destroy panets within a certain radius. (a wavefront from the explosion allowing you to evactuate a few planets would be cool)

An incredibly powerful slow, single ship go on a rampage through the universe (what is it looking for)

An enormous ammount of dark matter forms in an area of space that is slower to travel through. (perhaps with a technology that cancels it)

A single or group of minor races gets tired of being victims and forms an alliance, becoming a major race with colonization, invasion, etc abilities.

Humans and Altarians discover they Are the same race, political/cultural chaos ensues.

Race specific major events would be nice (eg Drengin splits into Clans, some of which are minor races, but an attack on one is an attack on all (in the mean time being they war with each other)

An asteroid headed towards a major world is discovered, it needs to be destroyed or that world will lose all it's buildings and half it's quality.

The aforementioned permanent Wormholes (btw a ship transportation technology with short range wormhole capability, but perhaps a "chargeup" time and a large size would be very interesting. Or a new type of starbase that can link to another of it's kind...

A race of organic based aliens invades the galaxy, they attack every inhabited planet, leaving it a barren wasteland before moving on. Growing more powerful as they advance.

An incredibly rich ring of asteroids is discovered in a remote star system, whoever controls this ring will become incredibly rich.

The ultimate weapon is discovered. It can't be reproduced, but you might be able to fit it to one of your capital ships...or they might.

The yor and Dark Yor are affected by a computer Virus, they reunite, double their productivity, and attack everyone, refusing to communicate. A spy might be able to introduce the fix to the virus. (leaving the Yor very grateful)

A blackhole forms from a supernova near the middle of the universe. It's dangerous to get too close...and what are the strange emissions we're recieving from nearby?

Several star systems have been randomly teleported throughout the universe. We call it the "Jiggy Effect" it's disrupted the previous order of the galaxy in any event.

A spaceship derelict larger than any manufacturable by the known races has been discovered drifting through space, if a race can salvage it, they might discover a new ship class...

A new race is attacking from the 5th dimension, we don't know how to defend ourselves (perhaps wormholes will help?)