You've installed the PDF iFilter on the server and registered the dll.... you've added the icon to the images folder and the reference to the xml file... you've added the file type in the Shared Services provider Search Settings... you've run the full search indexing for the portal...

...the icon for pdf will display correctly in lists & libraries....but you *still* don't get pdf documents appearing search results??

You wouldn't happen to be running a 64bit server for SharePoint or SQL ??

If you are then there's some bad news for you. Adobe have not yet released a 64bit version of the iFilter for PDF. And while the 32bit version installs without error you will not get any results appearing in the SharePoint search.
As yet Adobe have not announced when (or even if) they will release this.

In the meantime there is an alternative.... Use this 64bit iFIlter from Foxit Software

Note: the installer does not register the application with MOSS 2007. After installing you will need to manually add a pdf extension in the registry settings:

  1. Open regedit and locate the following:
[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Shared Tools\Web Server Extensions\12.0\Search\Applications\<SiteID>\Gather\Search\Extensions\ExtensionList]
  2. Add a new String value with the latest number in the sequence and edit it to add pdf as the Value data.

Then, check that the pdf file type shows in the portal Shared Services Administration:
  1.  Under Search click Search Settings
  2.  Under Crawl Settings click File Types

If not then add it:
  1.  Click New File Type and add pdf

Incidentally, this will add the following reference for the pdf file type in the registry:
  1. Open regedit, locate [HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Office Server\12.0\Search\Setup\ContentIndexCommon\Filters\Extension\.pdf] 
  2. Check the default value is {987f8d1a-26e6-4554-b007-6b20e2680632}

Check also that you have the .gif file that you want to use for the pfd icon in the following folder on the server: 
  Drive:\Program Files\Common Files\Microsoft Shared\Web Server Extensions\12\Template\Images

(the icon can be found here (use the 17 x 17 one): http://www.adobe.com/misc/linking.html)
Then: 
  1. Edit the Docicon.xml file to include the .pdf extension. To do so: 
      Start Notepad, and then open the Docicon.xml file here: Drive:\Program Files\Common Files\Microsoft Shared\Web server extensions\12\Template\Xml 
  2.  Add an entry for the .pdf extension. For example, where NameofIconFile is the name of the .gif file: <Mapping Key="pdf" Value="NameofIconFile.gif"/> 
  3.  On the File menu, click Save, and then quit Notepad. 

Next - REBOOT THE SERVER! (Before doing this there were a few minutes frustration. Simply stopping & starting the services, iisreset etc is not sufficient)

When rebooted go back to the portal Shared Services Administration and start a full crawl:
  1. Under Crawl Settings click Content sources and Crawl Schedules
  2. Click the arrow icon next to your Shared Service (Default name is: Local Office SharePoint Server Sites) and select Start Full Crawl