clean the whole thing and start over
You can clean and clean with spydoctor and antivirus, but you will never get rid of all of the problems now in the registry until you put in the backup install disk and reload windows and all of the other programs. Those programs may minimize the problem for a while, and you might then be able to load all of your "valuable" files onto an external hard drive, or some other resource, but the problems in the registry will continue to cause problems, like reloading the trojans, etc.
Just my two cents, but with my four kids and their four computers, I have found this to be the only real solution. Yes, I have PC Tools Firewall Plus and Avast, but still every 6 to 7 months, I find myself cleaning their computer. All of these great products still miss some items, and they build up over time.
And never, never load one of those "must downloads now".