My personal favorite and least favorite mega events, with favorite events not necessarily being "fun" as much as balanced and disruptive (like mega events should be):
- The Mega Pirates, for two reasons. Besides the obvious "really annoying reset button" aspect, the fact is that a player who knows how to exploit the pirates can turn this event into a giant "I Win" moment. The AI can't really adjust to the pirates and will never clear them out on its own, meaning that you can either finish off the pirates and emerge as the only civilization with a fleet, or just hunker down and go for the tech win.
- The "Depression" event that gives a global hit to morale. Unlike other state-changing events like the "Tourism Boom" or "Graft and Corruption" events, this one is all downside - and it never seems to end. Just really annoying.
(Dis)honorable mention goes to the "Subspace Tears" event that creates a permanent speed limit of 5. It's not entirely terrible (for one thing, it makes fighters much more valid as an option) but on the giant maps I like, it's just an incredible pain to deal with. This is one of those events I wish would scale.
- The Peacekeepers - unlike the pirates and their reset button function, the Peacekeepers actually don't destroy every ship in the galaxy. The event doesn't work like the text says (I don't know if this is a bug, or whether the event was changed and the text is an artifact of an earlier version) but it still is one of the best mega events at making a major change to the galaxy that doesn't completely unbalance things. I've only had them appear once, but it was a very interesting turn of events.
- The galactic plague/disease - now that the AI has been fixed to actually research the cure, the events are another good example of a mega event that shakes things up in a fair way (even if they are a little unrealistic). The disease in particular can have interesting results - on one occasion, it hurt the Drengin's morale so badly that seven of their planets actually revolted to form a new civilization - something I'd never seen before.
Honorable mention goes to the Dread Lords. They're very hit and miss - sometimes they get wiped out before doing anything, sometimes they become a minor nuisance before getting wiped out, and sometimes they actually turn into a real threat (once even becoming a menace on the level of the easier campaign missions, though not quite up to "Apocalypse" levels). Again, an interesting mega event - not always fun to deal with, but certainly does its job of making a major change to gameplay on the times they do come in strong.