I'll head out on a limb here and say any Registry worth cleaning, is worth scrapping!

Anti-Spyware. Virus Scans, Registry Tools, etc. do a considerably better job preventing attacks than fixing damage done, else they'd be their own Microsoft at that point.

The best way to recover from a bad registry is to modify your work flow:

1.) Never put anything of importance on the drive/partition you've installed Windows to. 

2.)  Always keep your Setup and Created files on a seperate mirror/drive/partition.

This way when infections occur recovery is as easy as deleting Windows drive(, because that is all that is infected.)  You'll need to install all of your programs again, but how many Maya, Poser, Vue, Premiere and/or Photoshops' do you have, before you've learned this lesson?

This way there is %0 chance the virus still exists.

I can FDISK(delete everything,) and Install Windows in less than an hour.  There are a handful of women on my street, with children whom love to eat cookies.  Every 6 months or so they ask me clean their PCs out.  CompUSA will do a Windows Install for about $80, so I do that and actually clean the inside of the computer(With an air compressor) for $40.  This is usually a good time for them to add Hard Drives, and RAM sticks too.  So, I get to clean my stock of older, unused purchases.

=  )