I voted for the Green Goblin Arc.
The Lizard Arc, while not bad by any merits, was a bit uninspired. No matter how you twist it, the main Lizard story is always basically the same and it's not the absolute best that Spider-Man's mythos can offer. Still, they made efforts with it, and it was as good, as it could have been, but the theme about normal guys turned into supervillains by accident - both the Lizard and Electro - is boring.
The Big Man Arc, I like very much. I actually wondered wether to vote for it, instead of the Green Goblin Arc, with which it is intertwined. I liked the idea that supervillains like Shocker, Sandman and Rhino were created on purpose with the sole idea of distracting Spidey. Nice spin.
The Green Goblin Arc, is my favorite by far. I liked the characterization of the Goblin - he was absolutely fearless and crazy villain. Can't wait to see him again. A nice theme in the Arc was how the supposedly weak people could become terrifying maniacs when the rights buttons are pushed - as it was shown not only with the Goblin, but with Dr. Ock as well.
The Symbiote Arc, while definately had its good moments, could have been handled a little better. I think that the turning of Eddie into Venom was rushed, given the fact that he didn't receive enough attention during the most of the first season. I think that they could have dragged the Symbiote Arc through the most, if not the whole, of the second season, by intertwining with its Arcs and making Peter go bad slower, and also ruining the life of Eddie more.
The Master Planner Arc I find... unsatisfying, so far. It's not bad - there is nothing bad in SSM, so far - only, it could have been better, I suppose. It lacks thrill and suspense. I hope it doesn't end completely with the next episode, bacause I don't think that only four episodes are enough for any kind of convincing Master Plan.