The season 2 finale where Clark's actions caused Martha to lose the baby. That was the best one hands down.
I voted Vessel because I was extremely excited about the coming of General Zod and then Commencement. Exodus was probably the most emotional and human finales because of what happens to all the characters in that episode.
For me, it was Vessel. This ep had a great pace, great Clark & Chloe scenes, and one hell of a final scene. That's how cliffhangers should be done.
That's not the greatest list. It's kind of a shame when non of a show's top five episodes are finales. Anyway, I voted for Commencement. It's the only one that really felt like a season finale in terms of it being grandiose and high in production value. Exodus and Vessel felt more like typical sweeps cliffhangers. Phantom was terrible and I still haven't even seen Arctic yet.