As with most things, it depends. I think if you want speed and interoperability (with other languages), use JSON, in particular JSON::XS.
If you want something that's only ever going to be used by Perl modules, stick with YAML. It's much more common to find Perl modules on CPAN that support data description with YAML, or which depend on YAML, than JSON.
Note that I am not an authority and this opinion is based largely on hunch and conjecture. In particular, I have not profiled JSON::XS vs. YAML::XS. If I am offensively ignorant, I can only hope I will make someone irate enough to bring useful information to the discussion by correcting me.
