See features here for a list of all file types it can index. Also, you can download plugins to extend GDS for just about every file format in existence.
If you don't want Google sniffing your stuffz, try Copernic. I'm almost certain it indexes PDF.
I know this isn't what you are looking for, but worse comes to worse you organize all the files in directories by category and use find. Also, using symlinks and hard links where applicable.
It'd totally be a bitch to organize, but it could be done over a period of time.
Also, this would help in the meantime. One way or the other, organizing all the files categorically in directories is a good idea, and once it is done it's easy to keep new files organized.
Edit - but I will be come Sept 14. won't the existing product keep on working? I guess eventually it may not be able to understand new versions of Office docs (current versions and pdfs should still work I imagine). Maybe they'll hand it over to the opensource community? Here's hoping!