http://www.phplinkdirectory.com/ (the most popular one as I see,you can use V2.1 for free) http://scripts.site-sift.com/ (In order to set this,you need an business paypal account) http://www.indexscript.com/download.php http://scripts.webmastersite.net/wsnlinks/ http://www.cplinks.com/ http://www.www.esyndicat.com Personally,I prefer Phpld.
Nearly free and one that looks the proverbial bollocks: http://www.indexu.net/ EDIT the banner you see there isn't linked to where you can get the script, it's here: http://www.nicecoder.com/
I think it's fantastic. I wouldn't really want much more than what it does. I mean... I wasn't even looking for a display of the PR and it shows them.
If you don't want it,you could take it off.. Admin--->System--->Edit Settings--->Directory---->Then you'll find some selection box besides "Show PageRank".Select "No" .