R-S nomenclature refers to the orientation of functional groups around the chiral carbon of an amino acid. Each group is assigned a priority based on the molar mass, from 1 to 4. When two identical atoms are bonded to the carbon, the next atom down is used to determine which is of greater priority. 1 refers to the heaviest, and 4 to the lightest, which will always be the chiral hydrogen.

After priorities have been assigned, the Fischer Projection of the molecule must be oriented in your mind so that the hydrogen is facing away, behind the carbon. This will leave three other molecules facing forward in a triangular arrangement. You have to remember the relative depth from this perspective of each bond to make sure you have them lined up correctly. Once the image is complete, look at the ordering of the first, second, and third priority groups. If it turns counterclockwise, the molecule is in the sinister configuration (sinister is the Latin word for 'left', it doesn't have anything to do with the malevolent intentions of the molecule or some such). If they are oriented clockwise, the molecule is in the rectus ('right') configuration.

These are usually shortened to R or S, thus giving the name R-S nomenclature.

Some extra information courtesy of HexFailure (thanks!), the process of determining rectus or sinster configuration can also be called the Cahn-Ingold-Prelog rules. One institution that refers to it as such is the University College London.