By its very nature (i.e. that it can neither be created or destroyed) mass-energy didn't "come from" anything. In some form or another it has always been around. Stephen Hawking recently described a phenomenon known as vacuum fluctuation in which particle matter seems to come out of seemingly empty space. Hawking and the scientists working under him discovered that even in a perfect vacuum in which all traditionally understood forms of matter and energy are absent, random electromagnetic oscillations are still present. These vacuum fluctuations are a form of energy which can be converted into matter in complete harmony with mass-energy conversion laws. In other words, the nothingness of a complete vacuum in empty space can and does produce matter in accord with Einstein's laws.
My personal extrapolation is this: If mass-energy cannot be created or destroyed, then the universe, in one form or another, has always existed. There was never a time when the mass-energy of our universe did not exist, even if it was just in the form of an empty oscillating vacuum.
CyrusThePersian