As I used to write many times on SpywareInfo.com's forums...MSCONFIG is not a solution. it's a diagnosis tool. Once you diagnose the problem, either uninstall or disable the problem startup items correctly, then return msconfig to normal operations state. As a home service tech for three years I actually "fixed" at least a dozen PCs were the user had "stopped" their problem with MSCONFIG...except in the process they also disabled their audio drivers, or print utility, or some other vital system service. The most fun was that disabling things with MSCONFIG didn't even stop half the crapware/malware/virii; most of them just recreated their startup entries automatically the moment it was missing anyway.
Cleaning a PC, or tuning, requires looking at data (hijackthis log, CCleaner, whatever tool does the job best nowadays), identifying the problem items, and correctly removing or disabling them. Step 2 (identifying) is the most difficult, and I dare say most home users wouldn't have a clue about what the dozens of startup entries and services actually do. Personally I think the $99 price tag to optimize a PC is a bit high, but then we charged $65/hr to do it at someone's home or business ($45 if they brought it to us), and most malware cleanups took 12-15 hours although we stopped charging at 4 hours.