Hi Jason,
I've been looking at directory scripts for years and there are a few good options available depending on just what you want to do with it.
First, take a look at
http://www.phpmydirectory.com/ and
http://phpyellow.com/
They've both been around a quite a few years and they make it rather easy to setup a standalone business directory.
If you're not crazy about those, do a search at
http://www.hotscripts.com/ for a php or asp classified program script and you should find a few other options geared just for a business directory or one that's easily modified to make a directory with.
You could also use a link directory like wsnlinks or eSyndicat for a business directory too. Google them and you'll find more info about 'em.
Lastly - if you want to manage articles or other content in addition to the business directory, I'd highly recommend Article Live from
http://www.interspire.com
I just bought their article management (cms) script this month for a local community/directory type site I'm working on and it's a great system that does just about everything I need. With the ability to create unlimited categories and sub-categories it's well suited to being used for a directory and I'm really quite impressed and pleased with it.
HTH,
Steve