Short answer

x.yyy.

Longer answer

Both schemes are simple and short. x.yy is shorter by a single digit, but it is prone to a trap. One day, when you want to update your 0.13 module with a minor change you might say to yourself, "Gee, it's such a minor change that I think I'll release it as 0.13.1 instead of 0.14. Semantic versioning and all that." So you did, and boom. PAUSE would accept it but would refuse to index it. Why?? You would scratch your head for a while. Turns out that according to version.pm, 0.13 > 0.13.1. Why??? Because 0.13 numifies into 0.130 and 0.13.1 numifies into 0.013001.

I've fell for it once (twice actually, before deciding to convert to x.yyy). It's amazing how many veteran CPAN authors fell for it. For example, here's Dave Cross in 2016. Others I've seen while browsing the MetaCPAN Recent page. My bad memory prevents me from remembering who and when, and I'm too lazy to check, but trust me it's embarassingly often.

You might argue it's a bug with version.pm or PAUSE or Perl for behaving unlike the rest of the world, but that's how versioning works in Perl so just avoid this trap and be done with this. You might also say, "I'll always increase the minor version and will never use x.yyy.zzz." But there's always the possibility thay you'll forget and do just that.

It's unfortunate that x.yy remains (by my guess) the most popular versioning scheme for Perl modules, but consider yourself warned.

More about versioning in Perl

Books can be written on and years can be spent debating about versioning and its best practices, including in Perl. If you want to read more, here are a few links to get you started:

Some related posts by yours truly: