<p>I'm writing an intranet application for a client and I want to give them the ability to configure through an admin interface, which users and user groups can access certain areas. What I'd like to know is the best way of storing the reference to the user or group that is assigned to an area of the intranet. </p>

<p>Should I be using the <strong>domain\username</strong> and <strong>domain\groupname</strong> strings or should i perhaps be using the fully qualified ad name ie <strong>ou=computer room;cn=blah</strong> etc?</p>

<p>I will be storing the reference in SQL.</p>

MOSS provides many
webservices
out of the box which make life a little easier.  They are always worth exploring.
For this particular instance, I think the article,
Getting a list of files from a MOSS document library using a SharePoint web service
, will be of assistance.  If this isn't your exact scenario, it will get you on the right track.
If the Document service doesn't help you, the Search service will I'm sure.  Check the documentation for usage.