The one we know for sure about is related to gravity -- you normally ignore it in particle physics, but there's a point where you can't do that: http://en.wikipedia.org/wiki/Planck_scale

Now, it's quite likely interesting stuff happens before that point! (Such as the extra Higgs suggested by supersymmetry.) And there are also other, complicated reasons to suspect that the Standard Model breaks down, to suspect that it is really what we call an "effective field theory".

That's all ignoring issues like dark matter or the neutrino mass, which are not predicted by the standard model. But it's kind of interesting that the model (in a certain sense) naturally limits its own predictions.