I normally wouldn't be this picky, but you were asking for comments on coding style, so I'd have this to offer:
GetOptions(
'help|?' => \$help,
'version' => \$version,
'man' => \$man,
'token-debug' => \$token_debug,
'glossary' => \$glossary_output,
'dictionary' => \$dictionary_output
);
This tends to be an easier-to-read way to format hash-like structures.
I also tend to put all of my commandline options into a single hash (%opt, or %arg, or something) when they're going to be global. This saves variable namespace, but may be a petty concern.