Well, the title doesn't deal with story arcs the same way superhero comics do, but I'd have to say my favorite right now are the most recent events in Walking Dead (which could be loosely considered an arc). Unlike most zombie titles, Walking Dead doesn't feature the main characters somehow trying to stop the zombies, or find cures or causes for the zombies, or running into a military installation to find out why there are zombies, etc. It's an ongoing chronicle of normal people just trying to survive.
Thusly, it reads more like a soap opera where changes to the story gracefully roll into other changes and events aren't so rigidly divided. At any rate, the most recent events revolved around the main characters finding some measure of safety in a prison compound, but through a series of events, they're discovered by the leader of a small town (who, of all characters ever shown in WD, comes the closest to being considered 'evil') nearby who wants all the resources in the prison for said town, if not outright moving the population of the town into it for more safety. The story evolves from mere competing for territory to outright hatred and vengeance on the part of the town leader against the main characters, resulting in a bloody showdown that reached its climax in the last issue. Pivotal characters (some around since the first issues) have been killed and the prison sanctuary invaded by zombies.
I'll add that Kirkman is a brilliant writer and doesn't insult the reader by being predictable by any fashion. His mantra with Walking Dead is that "no one is safe", even main/popular characters, and it makes for a very tense, engaging read.