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I don't have a strong background in physics, but instead I'm educated in biochemistry. A lot of the principles behind the methods we use in structural biology perplex me. To give two examples:

1) FT-ICR MS (Fourier Transform Ion Cyclotron Resonance Mass Spectrometry) involves trapping ions in a Penning trap, and detecting the frequency at which they orbit the trap's longitudinal axis with the induction of current on two 'peripheral' coils. If the ions are not in phase, the signal on both coils will add to zero. To get them in phase, a scan of electromagnetic radiation is shot at them, and they will absorb relevant frequencies to their cycle time. Why is this the case?

2) In NMR (nuclear magnetic resonance) we can fire radio frequencies at samples of huge numbers of atomic nuclei to put their nuclear magnetic dipole moments spins in phase.

By this logic, could we (with a brilliant enough light source) change the spin of the earth since it somewhat exhibit properties of 'bar-magnet' subatomic particle? I know this sounds dumb -- I guess what I'm looking for is... what is this property of charged particles that allows you to bring them positionally 'in phase' just by shooting them with light?

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The principle behind this is similar to the driven harmonic oscillator in classical mechanics in case that is more relatable. The energy of the electromagnetic radiation is absorbed when the driving frequency is close to the frequency of the free harmonic oscillator i.e. its resonance frequency. This is possible, because the electromagnetic field interacts with the electric or magnetic dipole moment of the particles.

Whether this causes the particles to be in phase depends on what you actually mean by being in phase. In your first example it is about the phase of their oscillation in regard to the spatial position. I'm not really familiar with cyclotron resonance but as far as I understand the excitation of the particles to a greater orbit leads to a higher probability of particles bunching in packets (please edit this part if it's wrong). I don't think all of the particles in the trap need to be in phase in order to produce a usable signal.

In the case of NMR being in phase means that the spins point in the same direction during the temporal dynamics. This entirely depends on the type NMR measurement you want to perform. In the equilibrium state, about half of the spins point in one direction and the other half in the other with a small imbalance that causes a net magnetization. These spins are therefore already in phase. For a $T_1$ measurement you would simply flip this magnetization by a pulse, which doesn't change the phase effectively. For a $T_2$ measurement the initial phase is also kept when the magnetization is brought into the equatorial plane by a shorter pulse. Subsequent pulses only lead to a refocusing of the individual phases, that are drifting apart in the subsequent dynamics (see pulse echo). Therefore it could be said that pulses in NMR suppress dephasing rather than setting a phase.

Lastly, whether the magnetization of the earth could be reversed by some electromagnetic pulses can't really be answered right now, as it is not understood what causes the poles to reverse in the first place. The current theory establishes turbulent plasma currents near the inner core as the main source for the magnetic field. So I guess you would somehow need to reverse the direction of those currents, which isn't quite the same mechanism as reversing the magnetization of a nuclear spin.

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