You are talking about simple harmonic motion, so my answer will focus on that and ignore molecular vibrations (that doesn't seem to be what you're talking about).
For starters, I think it's good to consider amplitudes. Although everything has a natural frequency, the amplitudes of vibration are usually very low, so much so that observing them is difficult. This occurs because in reality there is a dampening which decreases the amplitude of oscillation with time (due to air resistance and other dissipating effects). This means that if a damped oscillator is left on it's own it will have an amplitude close to 0, so we don't notice it. An ideal simple harmonic oscillator (no damping) would maintain it's amplitude forever if there are no external forces.
Regardless of if the amplitude decays, there is still a frequency of the oscillations. When left to oscillate on it's own (no external applied force), the frequency will be the "natural frequency". If you were to apply a periodic force with the same frequency, you will create "resonance". This can be explained through superposition. In the case of resonance you constantly have a steady amplitude that matches the systems amplitude, so the driving force keeps adding energy to the system, and the interference is always constructive.
On paper, without damping, the energy would increase forever. In practice this energy will eventually make something break, or just dissipate itself.
As far as your wrecking ball thing goes, you could do that. One problem will be controlling the vibration so it only effects your building, not other buildings in the area. Another problem would be controlling the collapse, it may be too unstable when resonating. A wrecking ball controls where you want to break next, doing so with resonance would require a lot of planning and may not be possible depending on how the system responds.
A third (and probably prohibitive economically) problem is the required force you need to oscillate the structure with to overcome its self-damping. A very small force would be easily damped out in the regular movement of the system. Maintaining a high-energy oscillation is quite unsafe; might as well use a wrecking ball or explosives.