I AM using PHPmyDirectory and I like it alot, speed is ok and everything else, as for customization these guys thought of everything, really powerful script. I recommend : see it at linkdor dot com , sorry I still can't post links in this forum
My pick is IndexU. They have a brand new release, an active forum, quick help desk responses and a reasonable price. Just my opinion, your mileage may vary...
before this try site-sift but when someone to hack, i change it to indexscript... (my paid directory) one my free blog directory using V3.3 phplinkdirectory, i think this script very good cause have they 3-party develop such mod, or tips-tips that they give to user
I will always vote for phpLD which got good support, lot of mods and designs. Esyndicat is a nice script but I had some really bad support experiences with that script to be honest and life is a hell tracking the updates.
It always makes me wonder when super old threads are re-opened with everyone vying in desperation to promote different scripts. I'm not even going to mention the script I work for, people will find us without having to and one newcomer summed it up nicely in this thread http://phplynx.com/forum/showpost.php?p=7052&postcount=1
Years ago I used phpLD. Seemed like a good option. You can also use Wordpress with some extensive theme design and adding custom taxonomies. I'd go with Wordpress now, maybe because in the past years it's the platform I have used the most.
If you want a more map based directory, we just released a new version of phpLD for this. http://www.phplinkdirectory.com/phpLD_Local_Released.php