The origin of all mass has been discovered: the Higgs Boson. More specifically, scientists have found the particle which slows down some forms of energy, but not others, to coalesce into mass. The particle was discovered by experiments at the Large Hadron Collider in Switzerland. The Higgs Boson was predicted by six physicists in 1964, including Peter Higgs.
The Higgs Boson creates what is called a Higgs field. It is similar to an electromagnetic field, when you pass near the magnet; you are affected by the field. The effect of a Higgs field is that certain particles are slowed down, like running in molasses. These particles form into mass, such as protons and electrons (more precisely the other bosons that construct them). Other particles, such as photons, pass through the Higgs field unaffected, and remain pure energy with no mass.
The discovery is a strong confirmation of the Standard Model of physics. It is the reigning theory right now, but still has some unresolved problems. It doesn’t include the ever elusive force of gravity, which acts differently than the other three forces (strong, weak, and electromagnetic). The discovery does go a long way to unify the electromagnetic and weak forces. This marks one step closer to unifying all of the forces in the holy grail of physics, the Grand Unification Theory. That ultimate goal essentially amounts to understanding how everything in the universe is connected.
How Stuff Works, What Exactly Is the Higgs Boson? http://science.howstuffworks.com/higgs-boson.htm
Fox News, 6 Implications of Finding a Higgs Boson Particle: http://www.foxnews.com/science/2013/03/14/6-implications-finding-higgs-boson-particle/