I've used only Getopt::Long. But it can use 'pass_through' option to let the unknowns without complaining. Read perldoc Getopt::Long for more explations on it.
Although since Getopt::Long is not that hard to use, I do suggest that you use for all situations. Since it allows easy way to bundle options and make your program work like pretty much any other "normal" commanline program (eg 'gnu_getopt' is good option).