What exactly are you trying to do - looking at solvent interactions in a MD trajectory? at solvent molecules visible in X-ray structures? At the degree of solvent exposure by residue orby atom in a structure? Depending on what you want to do, different programs may be optimal to answer your question.
In this case I would recommend VMD (Visual Molecular Dynamics) http://www.ks.uiuc.edu/Research/vmd/. In addition to the program itself, there is an extensive script library.