Subtle is the Lord by Abraham Pais (1982) page 85:
However, it became increasingly difficult in chemical circles to deny the reality of molecules after 1874, the year in which Jacobus Henricus van't Hoff and Joseph Achille Le Bel independently explained the isomerism of certain organic substances in terms of stereochemical properties of carbon compounds.
so it is quite cool to see that organic chemistry is one of the things that pushed atomic theory forward. Because when you start to observe that isomers has different characteristics, despite identical proportions of atoms, this is really hard to explain without talking about the relative positions of the atoms within molecules!
TODO: is there anything even more precise that points to atoms in stereoisomers besides just the "two isomers with different properties" thing?
Small microscopic visible particles move randomly around in water.
If water were continuous, this shouldn't happen. Therefore this serves as one important evidence of atomic theory.
The amount it moves also quantitatively matches with the expected properties of water and the floating particles, was was settled in 1905 by Einstein at: investigations on the theory of the Brownian movement by Einstein (1905).
This suggestion that Brownian motion comes from the movement of atoms had been made much before Einstein however, and passed tortuous discussions. Subtle is the Lord by Abraham Pais (1982) page 93 explains it well. There had already been infinite discussion on possible causes of those movements besides atomic theory, and many ideas were rejected as incompatible with observations:
Further investigations eliminated such causes as temperature gradients, mechanical disturbances, capillary actions, irradiation of the liquid (as long as the resulting temperature increase can be neglected), and the presence of convection currents within the liquid.
The first suggestions of atomic theory were from the 1860s.
Tiny uniform plastic beads called "microbeads" are the preferred 2019 modern method of doing this:
Original well known observation in 1827 by Brown, with further experiments and interpretation in 1908 by Jean Baptiste Perrin. Possible precursor observation in 1785 by Jan Ingenhousz, not sure why he wasn't credited better.
Video 1. Observing Brownian motion of micro beads by Forrest Charnock (2016) Source.