Before I answer, a couple caveats:
- As Adam said, the universe isn't going to start behaving any differently because we discovered something.
- Right now it seems much more likely (even by admission of the experimenters) that it's just a mistake somewhere in the analysis, not an actual case of superluminal motion.
Anyway: if the discovery turns out to be real, the effect on theoretical physics will be huge, basically because it
has the potential to invalidate special relativity shows that special relativity is incomplete. That would have a "ripple effect" through the last century of progress in theoretical physics: almost every branch of theoretical physics for the past 70+ years uses relativity in one way or another, and many of the predictions that have emerged from those theories would have to be reexamined. (There are many other predictions based on relativity that we have directly tested, and those will continue to be perfectly valid regardless of what happens.)
To be specific, one of the key predictions that emerges out of the special theory of relativity is that "ordinary" (real-mass) particles cannot reach or exceed the speed of light. This is not just an arbitrary rule like a speed limit on a highway, either. Relativity is fundamentally based on a mathematical model of how objects move, the Lorentz group. Basically, when you go from sitting still to moving, your viewpoint on the universe changes in a way specified by a Lorentz transformation, or "boost," which basically entails mixing time and space a little bit. (Time dilation and length contraction, if you're familiar with them) We have verified to high precision that this is actually true, i.e. that the observed consequences of changing your velocity do match what the Lorentz boost predicts. However, there is no Lorentz boost that takes an object from moving slower than light to moving faster than light. If we were to discover a particle moving faster than light, we have a type of motion that can't be described by a Lorentz boosts, which means we have to start looking for something else (other than relativity) to describe it.
Now, having said that, there are a few (more) caveats. First, even if the detection is real, we have to ask ourselves whether we've really found a real-mass particle. The alternative is that we might have a particle with an imaginary mass, a true tachyon, which is consistent with relativity. Tachyons are theoretically inconvenient, though (well, that's putting it mildly). The main objection is that if we can interact with tachyons, we could use them to send messages back in time: if a tachyon travels between point A and point B, it's not well-defined whether it started from point A and went to point B or it started from B and went to point A. The two situations can be transformed into each other by a Lorentz boost, which means that depending on how you're moving, you could see one or the other. (That's not the case for normal motion.) This idea has been investigated in the past, but I'm not sure whether anything useful came of it, and I have my doubts that this is the case, anyway.
If we haven't found a tachyon, then perhaps we just have to accept that relativity is incomplete. This is called "Lorentz violation" in the lingo. People have done some research on Lorentz-violating theories, but it's always been sort of a fringe topic; the main intention has been to show that it leads to inconsistencies, thereby "proving" that the universe has to be Lorentz-invariant. If we have discovered superluminal motion, though, people will start looking much more closely at those theories, which means there's going to be a lot of work for theoretical physicists in the years to come.