I use Free AVG AntiSpyware and have for some time deleted all that it finds. As to your worry, I don't have that worry since my files are all backed up and I can reinstall the OS if need be. But having said that I have yet to bust the OS this way. In fact I'm typing from my desktop that the OS was installed 4 years ago.
My computer is a PIII, 800mgh running on Win XP. Norton pick up a trojan called trojan/syp.win32@mx. All of sudden I have limited or no connectivity with internet. I ran Adaware and it found nothing. I went online with another computer and found a fix called Winsockxpfix.
I ran the program, rebooted and voila the problem is fixed and I am back online. I updated Adaware and ran the program and it found files and folders called Virusburst and win32.trojandownloader.zlob in the regvalues and regkeys. Should I delete or quarantine these keys or should I leave them alone because Winsockxpfix fixed them all? The trojandownloader obviously corrupted these files. Should I update Norton now and scan the computer and do what it says? I don't want to delete anything yet until I am sure that it won't take the computer back to where it was before.