Electronic structure calculations using the local density functional method with non-local norm-conserving pseudopotentials, ab initio molecular dynamics simulations, and a novel method of all-quantum simulations, combining a quantum path-integral description of the nuclear degrees of freedom with concurrent electronic structure calculations of the Born-Oppenheimer potential energy surface, were employed in investigations of the structure and dynamics of protonated water clusters. Using electronic structure, structural optimization and all-quantum simulations, structures and energetics of H3O+, (H2OH+, as well as NH4+, (NH3H+, and the mixed (NH3)(H2OH+ cluster, are described and analyzed. The quantum nature of the hydrogens in the protonated water clusters, as well as a measure of the tunneling enhancement of the inversion isomerization in H3O+ at 150 K, are demonstrated and discussed.