I agree. That was a good episode. The fact that it was left with no explanation makes it even worse. The fridge brilliance page at tvtropes has a few thought provoking comments on the episode.(cntrl+f and search for 'Midnight')

Oods are just good guys who lashed out because they were abused. I would too if I was made into a slave and had my brain cut out and stuff. They're not villains at all, they were just a product of their situation and once they were freed they became very peaceful and good. I love the Oods as well.

I liked all the Sherlock Holmes references in the Snowmen episode. I also liked the idea of the villain being a material projection of his own mentality. Those kinds of episodes are fun and make you think about stuff. I wouldn't count The Great Intelligence as my favorite though. It's been a while since I watched it though and I don't remember the episode too clearly. I remember being so excited when I finally got a chance to watch the new episodes!