Mine would have to be Seppias death, barcas death and the scene where spartacus is speaking to varro in the pits where varro is trying to give him he mandrake root while spartacus is hallucinating.
One of my favorites was when Spartacus was reunited with his wife, even though she was dying. So much was said without words, and then all he said was "I'm here."
Someone touched on a funny part, when Laeta was pitching her tent and it fell done, then Agron comes to help her, says Spartacus has feelings for her, and he tell hers "I would not have your feelings upon the subject." The expression on his face was hilarious.
Enid: So what was all that about enlarged holes and tight cracks? -Ghost World
The death of Cossutius, aka Rape Face. That dude was so evil that he's probably the most hated character in the series, which is a feat unto itself, but even more impressive when you consider he was in only a handful of episodes. The dude even spawned a meme for being such a sadist with the rapiest face imaginable.
And he died in a fantastic episode, which was the S2 destruction of the arena. I thought S2 was a bit shaky as the series found its footing again after Andy's death, but that episode was spectacular.
Everyone has mentioned so many great scenes, yet I also liked the bits in War of the Damned when Spartacus was experiencing the conflicts of being the leader of a full-fledged army and becoming no better than the Romans themselves (like with the brief games where they execute the captured Romans).
I also liked the bit when the mortally wounded Spartacus looks at the last remnants of his army.