I finally found the fix to the problem. Problem was i was running wss 3.0 in windows server 2008 r2 with ifilter6. Problem got solved after i uninstalled ifilter6 and installed ifilter9( This is the Most since you are running Windows Server 2008 r2). After that i made entry in \HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Office Server\12.0\Search\Setup\ContentIndexCommon\Filters\Extension and entered string 38 with pdf value.
After that
In the registry editor go to: HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Shared Tools\Web Server Extensions\12.0\Search\Setup\ContentIndexCommon\Filters\Extension.pdf.
b. Modify or create the entry and replace the values with the following.
Name = Default
Type = (In SharePoint 2010 this is created by adding a Multi-String Value)
Data = {E8978DA6-047F-4E3D-9C78-CDBE46041603}
PLease remember to replace the default value with this guid {E8978DA6-047F-4E3D-9C78-CDBE46041603}. This will ask sharepoint search service to use ifilterpdf9 instead of default search service.
After that i restarted search services and applied
Stsadm -o spsearch -action fullcrawlstart
Finally it started crawling the pdf. In some circumstances you also might need to reboot the server.
Thank You everyone for your help.