In Charles Stross's "Accelerando" (strongly recommended!) astronomers suspect that the inhabitants of Andromeda Galaxy converted all its baryonic matter to computronium (here: configuration of matter capable of the most efficient computation as per the laws of physics) and are using it to run a massive side-channel attack, trying to verify if the Universe runs on a virtual machine (and I guess maybe break out of it).
On a different note, here's a sobering thought for the Universe-as-simulation optimists: while it's possible the simulation's Creators wish us well, e.g. will store your soul/mind and let you live carefree in a Paradise... it might rather work like our current massive simulations (e.g. the Millennium Run [0]). It generates enormous amounts of data, but only some small amount (like a state snapshot every 100M years) is actually captured and analyzed. I.e. the "dumb" computing power at the Creators' disposal is far greater than their mental capacity. The whole existence of humanity might go unnoticed, just a side-effects of the simulation's fidelity.