The UI version has a simple interface:

You can select individual files or wildcards to find input javascript files.
The command line version has the following syntax:
JsMinifier.exe "input js file" "output js file" NoUi
Like the UI version the files specified can be wildcards. If wildcards are specified you can omit the output file - the files will be created in the same directory as the source file.
The default extension for the generated files is .min.js.