I'd like to increase the hydrophobicity of a glass substrate (or lower the surface energy) without adding any coatings / layers. What are some common methods to achieve this?
Without changing the chemical structure of the glass surface, it cannot be made hydrophobic. For example, if you melt the surface, treat with ionizing radiation, the hydrophobicity will not appear. You can try to get a surface similar to the surface of the lotus petals, but is it possible? Try it.
Without any coatings, that is going to be difficult because a flat glass surface is the most hydrophobe structure that you can get to my extent of knowledge. As soon as it gets rougher, the surface will become more hydrophile. The only small difference is the doping degree, so pure Quartz glass is has the highest surface energy (DOI: 10.1111/j.1151-2916.1969.tb13350.x) while any doping will decrease it.
Maybe you can change the surface mophorlogy. The hydrophobic surface can be achieved by many states, such as Wenzel state, Cassie state. Generally, coarse surface can make the apparant contact angle become smaller accroding to Wenzel equation. However, if the surface is porous enough, that means the surfacce is composed of two components: glass and air. According to the Cassie-Baxter equation, hydrophobic surface can be obtained.