I like 2&3, nukes not only do a lot of damage lasting lifetimes, but MAD would leave nothing for no-one. 

I like the virus idea as a way to wipe 80-90 percent to allow for the natural immunity of humans as well as introduce the mutations for others to use. I'm curious how close to 'borderlands' this will get. Teleporting weapons hyper-tech but still having to hunt for food to eat diner tonight.

A meteor storm bombardment could be a good #3 all the big name superheroes died off taking out the biggest meteors miles across but a day long orbital bombardment of Volkswagen bug meteors would burn down to basketballs through the atmosphere and still rip right through buildings in a carpet bombing of doom.