I have a program that has to read a configuration file from a PHP script, and a quick search has revealed there are dozens of ways to handle configuration files in Perl:
If the audience is technical (used to formatted data structures), then I like using JSON for configuration. In your program it'll work like if you used YAML, but to me it's easier to read (and we use lots of JSON anyway).
If you use JSON::XS there's a "relaxed" option that'll allow comments and trailing commas and such in the files.