<p>Is there any sort of "out of the box" system within SharePoint (i.e. MOSS 2007) that is useful for tracking/managing permissions.  We've got a relatively small installation, but I can easily see special permissions for special users/sites getting out of hand.  I'm hoping there's something pre-baked into SharePoint that will help with this, but if there is, I don't know where.  </p>

<p>If this isn't available from SharePoint, are there any 3rd party tools people would recommend?</p>

Unfortunately, I haven't found anything that great out of the box in SharePoint for managing or tracking user permissions. You always have an opportunity for customizations. There are some third party tools, however. The best tool I've found for simple management of SharePoint is the Universal SharePoint Manager v2007.
This app has some stellar tools for analyzing security and information about permissions.
Here's a link directly to the feature that might interest you the most:
http://www.idevfactory.com/products/uspm2007/features/sharepoint%20user%20site%20security%20analyzer.aspx
I haven't used the USPM myself. I have used the SWAT tool which has a subset of features. iDevFactory does do a good job with their apps and I've found that it's fairly decent ant getting what you want.
Good luck!