"Best" is personal opinion. There are several good ones out there and each has its features, strengths and weaknesses. You might try testing some of the free/demo versions of available scripts and see which one suits you best.
This question gets asked a lot here. If you do a search for it you should get a great deal of information to help you.
the best really depends on the type of the directory you are planning to start (niche, article or even general) and depending on that you should consider PhpLD, PhpLB, esyndicat and edirectory.
Scooby gave a nice answer but still there are lots of directory scripts like phpld, esyndicat, indexU, skalinks. You can check a list of them in here. Directory Scripts
phpld directory script is the best, and is used by most of the directory owners, and then it's esyndicat.
Ummmm excuse me dont get "john luke " captain picard involved in this Im a treky from way back As for the script... they are all the same thx malcolm