Different ways to encode qubits in ion energy levels are sketched here:

In 40Ca+ ions, the quantum information is
(a) encoded in superposition states of the S1/2 ground state and the D5/2 state, the qubit is coherently manipulated with a laser near 729nm. See for details: S. Schulz, et al., "Sideband cooling and coherent dynamics in a microchip multi-segmented ion trap", New Journal of Physics 10, 045007(2008)
(b) A Raman transition between both Zeeman ground states m=+1/2 and m=-1/2 of the S1/2 can be used. The advantage is that Lamb Dicke parameter is larger by a factor 4 and thus faster gates are possible. Second, the required high relative phase stability of both Raman beams is easier to establish as the phase stability of the laser source for the optical transition near 729nm. Forqubit state discrimination, a rapid adiabatic passage pulse from the m=+1/2 state to the D5/2 state is applied and only then the fluorescence of the ion crystal is observed under excitation with laser light near 397nm and 866nm. See for details: U. G. Poschinger, et al.,"Coherent Manipulation of a 40Ca+ Spin Qubit in a Micro Ion Trap", arXiv 0902.2826
(c) Yet another approach is using hyperfine levels of the ground state e.g. in 9Be+ in the Boulder, 43Ca+ in the Innsbruck group.