system restore does "clean" up the registry--kind of, ...but it DOES NOT delete embedded files that hide in places like My Documents or random files in the program files folder under the C: drive. Microsoft will Flat out TELL you it wont delete, word files/documents, e-mails, or anything stored in the my documents folder nor is it supposed to clear anything that is installed on the desktop.
and I assure you, you will NOT have any success with restore if you have received the win32.exe or any of its variants or similiar trojans, they are called trojans because they are hidden. The win32 strain has its own VERY WELL hidden spawn that reproduces the registry key.. you may have seen it manifest as a pop-up that emmulates a valid windows warning message (similiar to the update warnings, etc.,) saying you do NOT have virus protection OR, it will re-route you to a web page of any NUMEROUS genre's. Malware writers are MUCH smarter than you are obviously giving them credit for and they have researched and Studied the weaknesses of the aprticular OS or system they are attacking.
in the best case scenario, If you are infected with a trojan, there may be a random file in your program files folder or your "windows" folder that looks like a harmless .exe or other "unidentified" files.. DELETE those manually, do not single click on them.... You MUST know what you are looking for if you are going to go into the WINDOWS area.... the programs on the market are much better and MUCH smarter than 90% of the computer users out there.
Programs Like SpyBot are aggressively updated and should be used regularlly ESPECIALLY if you go to **** sites, use P2P share sites/ programs, etc, or download from "cracker" or hacker sites.