Most C. elegans labs do large scale screens for mutants, gene upregulation, downregulation or developmental effects (smaller or longer body. Most of these were done under a microscope by an individual in the lab. The size of worms- about 1mM for the adults- makes them too big for cell sorters commonly available in most University or med Center setting.
Union Biometrica makes large particle flowcytometry instruments for C. elegans, fruitfly, mosquito larvae etc.
C. elegans worms could be sorted on the basis of size (embryo, larval stages, adults), level of reporter expression as well as dual color analysis (green and red, green and yellow).