Protonated complexes are produced via arc discharge in a molecular beam apparatus and probed using infrared photodissociation spectroscopy. The effects of protonation on the relative energies of the cis and trans configurations of protonated glyoxal are investigated with theoretical calculations. Upon protonation, the cis configuration is lower in energy than the trans configuration. Protonated hydrogen clusters are studied, and the spectra are assigned with the help of anharmonic theory. The structure of H5+ is a shared proton between two hydrogen molecules, while larger hydrogen clusters have a H3+ center solvated by neutral hydrogen. The effects of solvation, such as charge delocalization and polarization, in mixed protonated benzene-water clusters are also investigated.