These programs are only sparsely documented, sorry. If you are interested in using them to contribute to distributed computing projects then http://www.mersenneforum.org or http://www.primegrid.com are good places to get started.
If you are working with an exiting distributed computing project then the project administrator will have instructions posted somewhere about which program to use and how to use it for that particular project.
Otherwise you can probably figure out what you need to know by reading the README files included with the executables, invoking the program with the --help switch, or a little trial and error.
Note these files were moved here after GeoCities closed down. Any references to the url http://www.geocities.com/g_w_reynolds/ should be replaced with the url http://sites.google.com/site/geoffreywalterreynolds/programs/.