Antibiotics certainly has affected more people in a positive way, but I thing I too must vote for quantum mechanics. It fundementally changed the way scientists looked at the universe at a point where they thought they were just about out of new things to discover.
The realization that God's universe is truly complex, grand, and magnificent!(through the limitations and shortcomings of human scientific understanding)
I would have to add relativity as well... Of course, you could always say the biggest breakthrough in the last 100 years was Einstein -- and doubt their would be much argument.