Whatever method you're using to call the command line tool can just call it multiple times. How were you planning on using it?
You could also setup a .bat file on windows or a shell script on the mac to process the entire contents of a folder if you wanted.
I've been wondering the same thing. Nicholas makes a reasonable point, except that I was under the impression that Filemaker client's batch processing also took care of data references among the files in the batch, and I don't see how the Standalone Converter does that, even with a looped batch file of one's own that repeatedly calls the Standalone Converter.
With that in mind, my sense is the Standalone Converter is useful for enormous, single-file monolithic solutions conversion, rather than the folder-full-of-files solution.