I recommend JOpt SimpleJOpt Simple. It 'attempts to honor the command line option syntaxes of POSIX getopt() and GNU getopt_long().' It has community traction and notably is the command line parsing lib of choice for the OpenJDK itself.
For comparison, here's a relatively up to date (as of Jan 2015) list of related libraries that serve the same purpose.
- picocli (with ANSI colors and autocomplete)
- JArgs
- Jakarta Commons CLI
- TE-Code (it has a command line parsing library.)
- argparser
- Java port of GNU getopt
- Args4J
- JSAP
- JOpt SimpleJOpt Simple
- CLAJR
- CmdLn
- JewelCli
- JCommando
- parse-cmd
- JCommander