James Henry blogged about how to enable PDF indexing in Sharepoint:

Here are best instructions for properly configuring SharePoint to search PDF documents and view the file type icon in a document library. This involves installing the Adobe PDF IFilter 6.0 on each SharePoint 2007 front end web server. You would also need to do this on the Search Server, if you have split this up in your environment.

Perform the following steps for either Windows SharePoint Services v3 (WSS v3) and Microsoft SharePoint Server 2007 (MOSS 2007).

• Download Adobe PDF IFilter 6.0
• Stop the IIS Admin service: Start -> Run -> services.msc -> IIS Admin Service -> Stop
• Run the Adobe PDF IFilter 6.0 Setup program to install the filter on the server
• Copy the ICPDF.GIF file ( – right click and save as) to "[Hard_Drive]:\Program Files\Common Files\Microsoft Shared\Web Server Extensions\12\Template\Images"
• Edit the file "[Hard_Drive]:\Program Files\Common Files\Microsoft Shared\Web server extensions\12\Template\Xml\DOCICON.XML"
  1. Add an entry for the .pdf extension.
     
• Perform an iisreset by performing the following: Start -> Run -> iisreset. You could also recycle the SharePoint Application Pools in Internet Information Services Manager

For MOSS 2007, perform the following additional steps

• If you have MOSS 2007 and have enabled Shared Services then, goto Central Administration -> Shared Services Administration -> Select your current Shared Services Provider -> Search -> Search Settings -> File types
• Click on the "New File Type" button
• Add the "pdf" file extension in the designated text box and click on the "OK" button
• Go back to the Search Settings page
• Click on the "Content sources and crawl schedules" link
• Select the content source, access its context menu, and click on "Start Full Crawl"

I use Sharepoint Services V3 and installed the PDF IFilter after I uploaded hundreds of PDFs. This was bad, because Sharepoint Services does not crawl these already uploaded documents until they are touched (modify a property or so). Since no GUI is available to do so like in MOSS you have to use stsadm.exe command which ships with sharepoint:

Change the directory to: Program Files\Common Files\Microsoft Shared\web server extensions\12\bin
Now execute: stsadm.exe -o spsearch -action fullcrawlstop
then: stsadm.exe –o spsearch -action fullcrawlstart