Here's something to consider...
Is your son at all aware of the news? Is it ever on when he's around, in earshot or eyesight, in your house? Is there any chance the kids are talking about the news on the playground right now?
Because there's some pretty scary stuff going on in the world right now.
There's earthquakes, tsunamis, volcanoes and the thread of a nuclear meltdown in Japan. There's civil war in Libya and airstrikes and planes going down. There was a big earthquake in New Zealand. There was a revolution in Egypt!
I know when my son was six, this kind of thing made him pretty twitchy. Especially when the news would feature traumatized orphans, and bloodied children, and women in refugee camps, crying for their dead husbands and brothers. Even when you try not to let your children see the news, the stress still comes through. They hear adults talking, and they talk about it with each other. Your son might not understand how far away all these tragedies are, or how safe HE is.
I thought of this too since you said you are pretty sure that nothing happened in school. Could he have seen some of the coverage of the tsunami? That could certainly be enough to frighten a child. I'm inclined to think that something triggered it since it is so late in the year and the routine has been established.
DS15 had separation anxiety in kindergarten, but at the beginning of the year. Two of the things that we did which seemed to help were to send him to class with a stress ball in case he felt anxious. We also let him bring a picture of us to keep on his desk.
Hope you are able to get things sorted out. It's so hard seeing your little one so upset.

