Abstract: Atomic gases and single photons are among the most promising candidates to implement quantum information technology because they can be well isolated from their environment. Despite this advantage it is challenging to design controllable interaction between these particles and to store or manipulate quantum information in a reliable way. We have explored how electromagnetically induced transparency can be used to create a large nonlinear interaction between single-photon pulses, to transfer optical states between different photon modes, and to create an unusual interaction between light fields. Furthermore, we have found new results on the physical limitations of decoherence-free states. The nature of these limitations points towards new directions in the search for decoherence-free subspaces.