Google is your friend: http://www.google.com/search?q=free...s=org.mozilla:en-US:official&client=firefox-a
How long until some tells the OP to just search digital point forums for this? If you do search you just end up with a bunch posts telling people to search, very funny. @shulink: Take a look at this guys blog post: A Complete List of Directory Scripts at http://www.blong.info/list-of-directory-scripts.php It's very comprehensive. Also for free scripts go to sorceforge and search for directory. There is the old 2.12 version of phpld called gpld available there for free as open source.
The one that gives you what your looking for PhpLD has a free one, ive only used the paid one but its good.
PHP Link Directory is surely the best directory software out there But PLD charge for every plugin they have IndexU was the one directory software that I consider a better substitute of PLD and which does not charge anything for Plugins Plus has some very good inbuilt tools
I think currently there are 3 major player: - phpld - indexu - esyndicate If you ask in this forum, you will get a lot of people vote for phpld. If you can describe more clearly what kind of directory site you want to build, than you will get more accurate answer because these 3 scripts has different kind of features set.
Bespoke as possible is always good. If you are submitting to directories seeing the same template over and over can be a little tiring ;-)
The template is not related with the software itself, it's just because most of directory owners are too lazy to have unique design. Because they will need to spend more time and money