Almost all substellar atmospheres are cool enough to form clouds from a variety of refractory and volatile materials; their temperature determines which species condense. Thick layers of dust, likely made of silicates, blanket hot substellar atmospheres, substantially changing each object’s spectrum. In colder objects, like the solar system planets and cold exoplanets, the silicates will be condensed well below the photosphere, with volatile clouds condensing in the photosphere above. Cloud chemistry and microphysics is challenging to model from first principles; clouds clearly form, but the specific species that condense at the high temperatures of most exoplanets are not well-constrained from theory. This uncertainty is a major barrier to understanding exoplanet atmospheres, since the clouds that form change our interpretation of a planet’s spectrum, including the abundances of molecular species and temperature structure of the atmosphere. The next key step in understanding these clouds is to empirically determine which clouds form using mid-infrared spectroscopy to identify mineral species. Currently there is tentative evidence from Spitzer that silicate features are present in hot brown dwarf spectra; these brown dwarfs have the same temperature atmospheres as many exoplanets. JWST will allow us to measure these silicate features in many hot brown dwarfs at higher resolution and high signal-to-noise. JWST will also allow us to measure these features for some directly-imaged planets. We present our simulations of model emission spectra, exploring the impact of individual cloud species, including how particle sizes, cloud composition, and cloud crystal structures change spectral features. We investigate which objects are most ideal to observe, exploring a range of temperatures and surface gravities. We find that silicate, corundum and perovskite clouds have a strong cloud absorption feature for small particle sizes (<1 um). Silicate clouds strongly absorb at 10 um while corundum and perovskite absorb at 11.5 um and 14 um respectively. We simulate observations using the MIRI instrument on JWST for a range of nearby cloudy brown dwarfs, including time-series observations for photometrically variable brown dwarfs which likely have patchy clouds. Our predictions suggest that with JWST we can uniquely identify a range of cloud species. Mid-infrared spectroscopy can be used to empirically constrain the complex cloud condensation sequence in substellar atmospheres.