Biggest Surprise/Best Moment: Death of Agent Coulson
Joss Whedon did a lot of unheard-of things with Marvel's The Avengers, but the one thing people don't mention is that he basically gave us a comic book crossover that didn't suck. And, like all comic book crossovers tend to do, Whedon (with some urging from Kevin Feige) went and killed off a beloved character in the midst of his big event. The shocker is that the director-writer did in Agent Coulson without making it feel like another thing to check off on the list. Basically, it's one of the few times that the stunts we usually have to endure from superhero "events" actually worked.
Runner-Up: Marvel NOW!
Marvel NOW! isn't a surprise because it happened, but because it has been quite good (at least for now). Most of the titles, especially Uncanny Avengers (Rick Remender), Indestructible Hulk (Mark Waid), and Thor God of Thunder (Jason Aaron), have been nothing short of brilliant mainstream superhero comics. The best thing about Marvel NOW! is the powers that be behind the initiative actually paid attention to, and learned from, the mistakes (which were legion) that DC Comics committed with their New 52 reboot. Proudly announcing that "this is still the same Marvel Universe that you grew up with," Marvel Comics managed to reinvigorate while actually telling some good stories starring their most high profile characters. And as for this long term "DC is For Me" comic book reader, I’m now crying "Make Mine Marvel" after several years of basically ignoring the publisher. If that statement isn't worth its electronic ones and zeroes in pure marketing gold for Marvel Comics then I don't know what is.