Database size issues aside, as that is a business / environmental issue, I would still give the Adobe iFilter a try.
We are a SaaS-based company, hosting databases for our customers. They have the ability to upload and store PDF documents, along with Microsoft Word and PowerPoint files. Our application also provides the ability to search over the content contained in these documents.
We're currently using 32-bit SQL Server 2005 with the Adobe iFilter that is provided with the Adobe Reader 9.1.
I am, however, a little bit suspect of Microsoft's use of Adobe's iFilter. (It is so encapsulated that there is little to do when something goes wrong).
The issue is generic, regardless of the iFilter provider. I.e., Microsoft's Office iFilter has the same limitations.