We report on the optical characterization and site-selective low-temperature spectroscopy of thionine, methylene blue, and oxazine-4 encapsulated in the nanostructured pore system of faujasite-type Na-X, Na-Y, and dealuminated SiAl(100) zeolites. If the porous crystals are saturated with coadsorbed water the properties of the samples are in general similar to solid solutions of the dye, e.g., they exhibit large inhomogeneous broadening and nonphotochemical hole burning. Dehydration of the samples induces a considerable modification of the guest-host interaction, e.g., suppression of nonphotochemical hole burning, changes in the solvent shift, and partial protonation of the dye. In the special case of thionine in zeolite Y, dehydration gives the chromophore additional degrees of freedom leading to two distinguishable ground-state conformations of the guest molecule in the porous host. Interconversion between these two conformations can be induced thermally as well as optically. Low-temperature high-resolution spectroscopy reveals persistent spectral hole burning as well as the phenomenologically opposite effect, i.e., antihole formation. Temperature-dependent measurements allow an evaluation of the energies and transitions involved in this bistable guest-host system.