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1. First, you need to download the Adobe PDF IFilter 6.0, which you can find at this URL.  You should also get hold of a suitable Icon to use with PDFs, so that when they are listed in a document library they are easily recognisable.  There is a 17 x 17 one available on the Adobe web site here.
2. Once you’ve downloaded the IFilter, install it on your WSS 3.0 server, and then follow the instructions on registry settings in Microsoft KB Article 927675.  I’ve always found that providing the Adobe IFilter installed properly, the only setting I need to add is the Search Extensions one listed in step 2.  Also note step 5 re stopping and re-starting the search service.
3. Now you need to set up the Icon file.  If you downloaded the icon file in step 1 above, you will have a file called pdficon_small.gif.  You need to copy this onto your WSS 3.0 server, into drive:\Program Files\Common FIles\Microsoft Shared\Web Server extensions\12\TEMPLATE\IMAGES.
4. Next you need to edit the XML file which WSS uses to link file extensions to icons.  This file is called DOCICON.XML and is located at drive:\Program Files\Common FIles\Microsoft Shared\Web Server extensions\12\TEMPLATE\XML.  Navigate to that folder and locate the file.  I would suggest making a backup copy first, then opening the file in NotePad.  You need to add a mapping key for PDFs at the bottom of the file, above the </ByExtension> closing tag.  The new key will be <Mapping Key=”pdf” Value=”pdficon_small.gif” OpenControl=””/> (note that XML is case sensitive so make sure you use same case as previous entries).  Then save the file.
5. That’s pretty much it, but if you already have PDFs uploaded to your WSS server I would recommend starting a full crawl.  You can do the with STSAdm, the command syntax is Stsadm -o spsearch -action fullcrawlstart .  More on this on TechNet here.

Source : http://workerthread.wordpress.com/2008/01/03/configure-pdf-ifilter-in-wss-30/

By default, the search service is disabled in WSS 3.0. In order to enable it, goto your SharePoint Central Administration page and under the Operations tab, goto the “Services on the Server” list and click on WSS Search.

• Service Account – You cannot use any built in accounts when specifiying the Service Account, however you can use local accounts. One account you can choose to use is the default Administrator account on your server, “myserver\Administrator”.
• Content Access Account – Use an account that has full read access to your SharePoint Content Databases. As a security precaution, try not to use an account that has write permissions on the database. For example: “mydomain\sqlserveruser”.
• Search Database – In most cases the default settings will work, change them as required.
• Indexing Schedule – No new files will be searchable until they are indexed, depending on the load you wish to put on the server you can set this to be done as often as you want.

Upon submitting the form, the search service should start and begin indexing the content in your SharePoint site. Now would be a good time to install the Adobe IFilter to allow your search service be able to index PDF files, the earlier you install it the better, since it will only recognize PDF files added after the addon was installed.

Source : http://geekswithblogs.net/karskip/archive/2007/11/30/117263.aspx