Both script providers with many referenced sites and testimonials, would imagine phpLD has the bigger user base But as for comparison have not used both so not qualified to comment
I really like phpmydirectory but it has one issue -- it does not has the capability for non-registered users to pay for site review. But otherwise it is very powerful and has more capabilities than a average directory script. -Princy
Since phplinkdirectory has a large userbase and modifications, templates and support available to it, I will recommend you to use PhpLinkDirectory.
Would you care to expand on that as I'm planning on doing a comparison chart of ALL scripts so people don't get bad advice.
If this would be my first directory I would go with phpmydirectory a little difference is good.(By the way both are good scripts I looked from a different perspective.)