(Skip to the bottom for a list of classical and quantum-mechanical effects of gravitation that have been observed in subatomic particles; my attempt to explain quantitatively what it would take to measure atom-atom gravity got longer than I'd intended, and I haven't had time to shorten it yet.)
Let's suppose you want to measure the gravitational attraction between two charged particles, with masses $m_1,m_2$ and charges $q_1e,q_2e$. The classical potential energy between the two particles is
$$
U = -\frac{Gm_1m_2 + \alpha\hbar c\, q_1 q_2 }{r}
$$
with gravitational constant $G$ and inter-particle distance $r$; the dimensionless fine-structure constant $\alpha\approx 1/137$ is defined by the relation $\alpha\hbar c = e^2/4\pi\epsilon_0$. The remarkable thing about this system is the weakness of the gravitational force: the Particle Data Group tabulates $G/\hbar c \approx 6.7\times10^{-39} (\mathrm{GeV}/c^2)^{-2} $, so for electric and gravitational interactions to take place at the same scale between similar particles, they'd need to have a mass-to-charge ratio of $m/q \approx \sqrt{\alpha \hbar c/G} \approx 10^{18}\,\mathrm{GeV}/c^2$. A proton has a mass-to-charge ratio of $0.94\,\mathrm{GeV}/c^2$, and a heavy nucleus might have $m/q \approx 200\text{–}240\,\mathrm{GeV}/c^2$ — a completely different ballgame.
In the land of electroweak interactions, we also have an interesting but feeble force which we might like to study against the overwhelming background of the electromagnetic and strong interactions. There we have the advantage that electroweak interactions strongly violate a symmetry, parity, which the electromagnetic and strong interactions do not. There's a whole class of experiments which put a polarized beam on a target and rapidly flip the spin of the particles in the beam, looking for a parity-violating asymmetry in the interaction of the beam with the target. The state of the art for asymmetry experiments is part-per-billion sensitivity. It's as if I gave you an "unfair" coin which, if you flipped it a billion times, would give you one more tails that heads. There's a fundamental limit to these sorts of experiments, known as counting statistics: if you are expecting $N$ identical-but-uncorrelated things to happen in a particular time interval, you typically get $N\pm\sqrt N$. In order to measure an asymmetry of 10–9, you're screwed by counting statistics unless you have at least 1018 events to compare; if you want "three-sigma significance" then you need another factor of $3^2=10$ more.
Remember that a mole — a gram of neutrons, or two grams of molecular hydrogen, or 27 grams of aluminum, and so on up the periodic table — only contains 1024 atoms. Confidently counting 1019 atomic interactions is no mean feat. It's doable, but typically takes about a decade of design work, a couple of years of data collection, and a couple of years of analysis.
This approach doesn't scale to gravitational interactions between charged atoms, for two reasons. The first is that the counting statistics is basically impossible, almost literally the square of the state of the art. If you wanted to look for a gravitational asymmetry in the scattering of lead ions, with $m/q=210$, you'd expect an asymmetry around $2\times10^{-16}$, and so you'd need somewhere around 1032 interactions — imagine thousands of tons of lead, examined one atom at a time. The second is that for an electro-gravitational asymmetry, the sign change is on the wrong term: rather than looking for a minute difference between two very similar events, you'd have to look for the same minute correction to like-charge and opposite-charge interactions. It's unlikely you could measure the two interactions with enough precision to be compared to each other. For instance, the rest mass of a Pb+ and Pb– ion are different by five parts per million, just because the one has two fewer electrons than the other.
Looking for gravitational interactions between neutral atoms would be easier, but not millions of times easier. Neutral atoms may still have magnetic moments, and can electrically polarize each other at close approach; these effects are well-described, but not described at the part-per-million level. Plus, neutral atoms are harder to push around than ions. Any real atom-atom gravitational experiment would have to go through many orders of magnitude of currently-unexplored effects of residual electromagnetism before gravity became measurable.
What you can do is to measure the gravitational attraction between one subatomic particle and the rest of the Earth, the same way that my bathroom scale measures the attraction between my belly and the rest of the earth. There are only a handful of successful experiments in what I think of as "semi-quantum gravity," showing quantum-mechanical effects in a Newtonian gravitational potential:
David Hammen's answer mentions the cesium fountain clock, in which a cloud of atoms is permitted to rise and fall under the influence of gravity, but that's essentially a classical effect. The cesium atoms rise and fall just like juggler's balls.
Similarly, I consider the Pound-Rebka experiment a classical effect. While the detection process in that experiment was scattering gamma photons from iron nuclei, the gravitational effect is a frequency shift which is also described by classical electromagnetism combined with general relativity.
The neutron interferometer experiment by Colella, Overhauser, and Werner (1975), and follow-on experiments, manifestly require both (newtonian) gravity and quantum mechanics. A horizontal beam of cold neutrons is divided and recombined by a single-crystal interferometer. The interferometer is rotated so that one outgoing beam is still horizontal, but vertically displaced. It costs the neutrons $mg \approx 100\,\mathrm{neV/m}$ to climb up the interferometer, so the neutrons that take the bottom path have ever-so-slightly less momentum, and therefore a different wavelength $\lambda=h/p$, than the neutrons that take the bottom path; this results in a shift in the phase of the interference pattern that depends on the angle between the interferometer and the horizontal. While the gravitational effect has been observed, it doesn't quantitatively match the prediction of the Schrödinger equation with a linear potential. Speculation in the community is that the interferometers (which are hand-sized, and weigh several ounces) twist when tilted, changing the spacing between the paths and introducing an additional phase shift.
Nesvizhevsky and collaborators (2002) (see also here or here) presented evidence that neutrons in a gravitational well may occupy only discrete bound states. They sent a horizontal beam of ultra-cold neutrons (total velocity ~ 5 m/s, vertical velocity quite small) through a narrow gap between a neutron mirror and a neutron absorber. When the gap was large, the neutrons could bounce off the mirror without touching the absorber and the transmission through the gap was large; when the gap was small, only neutrons with the smallest vertical velocities could shoot the gap without hitting the absorber. For gaps of a few tens of microns, the transmission shows evidence of becoming quantized: the transmission is zero up to a certain gap size, then steps up towards the continuum value as more bound states become available.
Building on this work, Jenke et al. (2011) have used a vibrating table to drive transitions between gravitational bound states. Greene points out that this is the first experiment ever to drive a quantum-mechanical transition without using an electromagnetic field, using only the strong and gravitational forces.