The initial fuel is Uranium...which decays into Plutonium. The Plutonium can also be used as fuel though. Some reactors require highly refined uranium, which is what is required for atomic bombs. I guess if they used lower grade uranium, it wouldn't really pose (as much of) a threat.
Modern nuclear reactors use fission (splitting atoms) which produces radioactive waste. That technology won't work for long - the amount of waste accumulating is too much, and you can't really safely get rid of it.
What needs to be developed is a stable nuclear fusion reactor. Fusion combines the nuclear particles, which releases energy. This is what happens in the stars (i.e. the Sun), and in nuclear bombs. Unfortunately, scientists haven't been able to figure out a way to control the reaction. The real benefit of fusion is that it produces very little waste in comparison to fission. Whoever figures out how to make a reliable fission reactor is going to be veryyy rich.