A theme would be a motif or special viewpoint of a story. In general a theme directs your thoughts toward an idea. Plants Versus Zombies is a theme around which the games of the same name are created. Galaga is a space shooting game where the theme is loosely Protect the Earth by Shooting Aliens. Angry Birds is just that, a bunch of birds that fly through the air, beating up pigs, trying to restore their eggs.
When it comes to jams like this, the theme will be a little more directed, I think. It will give us an avenue within which we can create a game. Something like Only the Brown Barrels. In this example, your game would include brown barrels in some capacity.
Hope that helps.