<p>When setting up a Home Directory on IIS6 properties for a web site there's an option to "Index this resource" which is checked on by default.</p>

<p>Microsoft's site says: </p>

<blockquote>
  <p>Grant this
  permission to allow Microsoft Indexing
  Service to include this folder in a
  full-text index of the Web site. When
  you grant this permission, users can
  perform queries on this resource.</p>
</blockquote>

<p>Can someone give me more information on when you would check this option on? What sort of queries would a user perform on this resource? What are the pro's and con's of having this set to on/off for a web site?</p>

This is for using the indexing service which used to drive the Search. I don't think anyone uses this anymore. It's pretty intensive against the HD. Check to see if the indexing service is even enabled on your server. We would disable by default.
If you open the indexing service mmc there will be a system and a web scope. Checking this box would add the web site to the web scope. If you were writing your own search algorithm, you would write a search query against the Web scope. Since it's 2008, you will use Google.