In this chapter a comparative study is presented between (I) sequential heuristics, (II) simulated annealing, (III) tabu search, and (IV) threshold algorithm for graph coloring and its application for solving the problem of the design of manufacturing cells in a job shop system production. The job shop production system has a very large proportion of all manufacturing activity. The principal concepts of manufacturing cells, graph theory, and heuristics are presented. The results obtained with these algorithms on several examples found in the literature are consistently equivalent with the best solution hitherto known in terms of numbers of inter-cell moves and dimensions of cells.