I've noticed that when the refs go into the huddle to break up a t.o. they hold their index up. Since they all do it, it appears to be a signs of some sort. What are they signifying?

It is to singal to the team that the "First Horn" has sounded.

Right. And you'll notice that they put two fingers up on the second horn. In media games, the ball isn't supposed to be put into play until then.

And they will NEVER hold up 3 fingers in that situation as it could be interpreted as "Read between the lines.";)

Better the index finger than the middle finger.