I think that the simulation hypothesis does not permit any evidence for or against that does not violate the laws of physics. There's no way to distinguish between being in a real universe, a discrete simulation of a continuous universe, a discrete simulation of a discrete universe, or a continuous simulation of either a discrete or continuous universe with limited measuring tools.
If the laws of physics starting changing in dramatically interesting ways, I might see that as evidence of simulation... and now I need to reevaluate the evidence about cold fusion in that light...
If it is... I hope they do not crash the system with the test.
http://www.huffingtonpost.co.uk/2012/12/12/physicists-universe-simulation-test-university-of-washington-matrix_n_2282745.html
Be sure to check out the actual reseach papers linked in the article! I would have linked to them directly, but the article is full of follow-on links of considerable interest.